user8157: In the Pali, nirujjhati (ni + rudh + ya) appears to be a verb for the noun "nirodha".

nirujjhati
ceases; dissolves; vanishes.
to be broken up, to be dissolved, to be destroyed, to cease, die

Uparujjhati (upa + rudh + ya) appears similar in etymology, however differs in the prefix.

uparujjhati
stops or ceases
to be stopped, broken, annihilated, destroyed

I have done some examination of the usage of these words in the Pali suttas and, for now, I think their meanings or usages are contextually different.
How can these two words be linguistically distinguished?

user471: According to the PTS Pali-English dictionary entry on the prefix upa-:

Upa -- [Vedic upa; Av. upa on, up; Gr. u(po/ under, u(pe/r over; Lat.
  sub fr. *(e)ks -- upo; Goth. uf under & on; Ohg. ūf = Ags. up = E. up;
  Oir. fo under. See also upari] prefix denoting nearness or close touch
  (cp. similarly ā), usually with the idea of approach from below or
  rest on top, on, upon, up, by. -- In compn. a upa is always contracted
  to upa, e. g. devūpaṭṭhāna, lokûpaga, puññûpatthambhita. -- Meanings:
  (1) (Rest): on upon, up -- : ˚kiṇṇa covered over; ˚jīvati live on (cp.
  anu˚); ˚tthambhita propped up, sup -- ported; ˚cita heaped up, ac --
  cumulated; ˚dhāreti hold or take up; ˚nata bent on; ˚nissaya
  foundation; ...

According to the PTS Pali-English dictionary entry on rujjhati:

Rujjhati [Pass. of rundhati] to be broken up, to be destroyed J
  iii.181 (pāṇā rujjhanti; C. expls by nirujjhati). Cp. upa˚, vi˚.

Uparujjhati means "upon ceasing" with "upa-" meaning "upon" or "on", more or less.
For example, from SN 56.22:

ceases with nothing left over.
asesaṃ uparujjhati.

This means nothing left UPON ceasing. "asesa" means nothing remaining.
According to the PTS Pali-English dictionary entry on the prefix ni-

Ni˚ [Sk. ni -- & nih -- , insep. prefixes: (a) ni down=Av. ni, cp.
  Gr. neio/s lowland, nei/atos the lowest, hindmost; Lat. nīdus (*ni --
  zdos: place to sit down=nest); Ags. nēol, nider=E. nether; Goth.
  nidar=Ohg. nidar; also Sk. nīca, nīpa etc. -- (b) niḥ out, prob. fr.
  *seni & to Lat. sine without].  ...

"Nirujjhati" means "breaks down" I think with "ni-" meaning "down", more or less.
From SN 12.62:

But that which is called ‘mind’ or ‘sentience’ or ‘consciousness’
  arises as one thing and ceases as another all day and all night.
Yañca kho etaṃ, bhikkhave, vuccati cittaṃ itipi, mano itipi, viññāṇaṃ
  itipi, taṃ rattiyā ca divasassa ca aññadeva uppajjati aññaṃ
  nirujjhati.

Here, the mind rises UP as one thing (uppajjati) and breaks DOWN as another (nirujjhati).

user13709: The difference is primarily in upa, which is used as an intensifier to designate the circumstance of cessation. Since it is an intensifier, we are led to read "obliteration" rather than "fading away" as for "nirujjhati", where the "ni-" is providing emphasis by repetition of meaning (i.e., ni- + rujjhati).
One can also feel the meaning of the prefixes "upa-" and "ni-" when performing physical actions:

Say "upa" when lifting or moving a heavy object. The breath is stopped briefly for exertion.
Say "ni" when putting that heavy object down. The breath is exhaled continuously and let go.


user43: They are not synonyms, they have different meanings derived from the same root and different prefixes.
Nirodha means stop, suppress, not allow to go on.
Uparodham means enclose, blockade. 
So aparisesa nirujjhanti means "completely stopped". 
But asesam uparujjhati means "fully enclosed".
So in DN11 the guy was asking about place where the physical processes are completely stopped (aparisesā nirujjhanti).
But Buddha said, that's not what we are talking about. It's about "place" where the physical elements have no footing, place inside which all concepts like beautiful, ugly etc., all namarupas, all conceptual discriminations are fully enclosed or fully en-scoped (asesaṃ uparujjhatī).
It is the universal space of information, the universal space of mind, is where they are all enclosed of course. When all discrimination is stopped and this "space" is seen in its original undivided way, is when the unborn/deathless is attained. It is this space is what we in Mahayana call Shunyata. 

8157: <p>In the Pali, <a href="https://suttacentral.net/define/nirujjhati" rel="nofollow noreferrer">nirujjhati</a> (<a href="https://suttacentral.net/define/ni" rel="nofollow noreferrer">ni</a> + rudh + ya) appears to be a verb for the noun &quot;nirodha&quot;.</p>
<blockquote>
<p><em>nirujjhati</em></p>
<p><em>ceases; dissolves; vanishes.</em></p>
<p><em>to be broken up, to be dissolved, to be destroyed, to cease, die</em></p>
</blockquote>
<p><a href="https://suttacentral.net/define/uparujjhati" rel="nofollow noreferrer">Uparujjhati</a> (<a href="https://suttacentral.net/define/upa" rel="nofollow noreferrer">upa</a> + rudh + ya) appears similar in etymology, however differs in the prefix.</p>
<blockquote>
<p><em>uparujjhati</em></p>
<p><em>stops or ceases</em></p>
<p><em>to be stopped, broken, annihilated, destroyed</em></p>
</blockquote>
<p>I have done some examination of the usage of these words in the Pali suttas and, for now, I think their meanings or usages are contextually different.</p>
<p>How can these two words be linguistically distinguished?</p>
 471: <p>According to the PTS Pali-English dictionary <a href="https://dsalsrv04.uchicago.edu/cgi-bin/app/pali_query.py?page=138" rel="nofollow noreferrer">entry on the prefix upa-</a>:</p>

<blockquote>
  <p>Upa -- [Vedic upa; Av. upa on, up; Gr. u(po/ under, u(pe/r over; Lat.
  sub fr. *(e)ks -- upo; Goth. uf under &amp; on; Ohg. ūf = Ags. up = E. up;
  Oir. fo under. See also upari] prefix denoting nearness or close touch
  (cp. similarly ā), usually with the idea of approach from below or
  rest on top, on, upon, up, by. -- In compn. a upa is always contracted
  to upa, e. g. devūpaṭṭhāna, lokûpaga, puññûpatthambhita. -- Meanings:
  (1) (Rest): on upon, up -- : ˚kiṇṇa covered over; ˚jīvati live on (cp.
  anu˚); ˚tthambhita propped up, sup -- ported; ˚cita heaped up, ac --
  cumulated; ˚dhāreti hold or take up; ˚nata bent on; ˚nissaya
  foundation; ...</p>
</blockquote>

<p>According to the PTS Pali-English dictionary <a href="https://dsalsrv04.uchicago.edu/cgi-bin/app/pali_query.py?qs=Nirujjhati&amp;searchhws=yes" rel="nofollow noreferrer">entry on rujjhati</a>:</p>

<blockquote>
  <p>Rujjhati [Pass. of rundhati] to be broken up, to be destroyed J
  iii.181 (pāṇā rujjhanti; C. expls by nirujjhati). Cp. upa˚, vi˚.</p>
</blockquote>

<p>Uparujjhati means "upon ceasing" with "upa-" meaning "upon" or "on", more or less.</p>

<p>For example, from <a href="https://suttacentral.net/sn56.22/en/sujato" rel="nofollow noreferrer">SN 56.22</a>:</p>

<blockquote>
  <p>ceases with nothing left over.<br>
  <em>asesaṃ uparujjhati.</em></p>
</blockquote>

<p>This means nothing left UPON ceasing. "<a href="https://dsalsrv04.uchicago.edu/cgi-bin/app/pali_query.py?page=89" rel="nofollow noreferrer">asesa</a>" means nothing remaining.</p>

<p>According to the PTS Pali-English dictionary <a href="https://dsalsrv04.uchicago.edu/cgi-bin/app/pali_query.py?page=351" rel="nofollow noreferrer">entry on the prefix ni</a>-</p>

<blockquote>
  <p>Ni˚ [Sk. ni -- &amp; nih -- , insep. prefixes: (a) ni down=Av. ni, cp.
  Gr. neio/s lowland, nei/atos the lowest, hindmost; Lat. nīdus (*ni --
  zdos: place to sit down=nest); Ags. nēol, nider=E. nether; Goth.
  nidar=Ohg. nidar; also Sk. nīca, nīpa etc. -- (b) niḥ out, prob. fr.
  *seni &amp; to Lat. sine without].  ...</p>
</blockquote>

<p>"Nirujjhati" means "breaks down" I think with "ni-" meaning "down", more or less.</p>

<p>From <a href="https://suttacentral.net/sn12.62/en/sujato" rel="nofollow noreferrer">SN 12.62</a>:</p>

<blockquote>
  <p>But that which is called ‘mind’ or ‘sentience’ or ‘consciousness’
  arises as one thing and ceases as another all day and all night.<br>
  <em>Yañca kho etaṃ, bhikkhave, vuccati cittaṃ itipi, mano itipi, viññāṇaṃ
  itipi, taṃ rattiyā ca divasassa ca aññadeva uppajjati aññaṃ
  nirujjhati.</em></p>
</blockquote>

<p>Here, the mind rises UP as one thing (<em><a href="https://dsalsrv04.uchicago.edu/cgi-bin/app/pali_query.py?qs=Uppajjati&amp;searchhws=yes" rel="nofollow noreferrer">uppajjati</a></em>) and breaks DOWN as another (<em>nirujjhati</em>).</p>
 13709: <p>The difference is primarily in <a href="https://suttacentral.net/define/upa" rel="nofollow noreferrer">upa</a>, which is used as an intensifier to designate the circumstance of cessation. Since it is an intensifier, we are led to read "obliteration" rather than "fading away" as for "nirujjhati", where the "ni-" is providing emphasis by repetition of meaning (i.e., ni- + <a href="https://suttacentral.net/search?query=rujjhati" rel="nofollow noreferrer">rujjhati</a>).</p>

<p>One can also feel the meaning of the prefixes "upa-" and "ni-" when performing physical actions:</p>

<ul>
<li>Say "upa" when lifting or moving a heavy object. The breath is stopped briefly for exertion.</li>
<li>Say "ni" when putting that heavy object down. The breath is exhaled continuously and let go.</li>
</ul>
 43: <p>They are not synonyms, they have different meanings derived from the same root and different prefixes.</p>

<p><code>Nirodha</code> means stop, suppress, not allow to go on.
<code>Uparodham</code> means enclose, blockade. </p>

<p>So <code>aparisesa nirujjhanti</code> means "completely stopped". </p>

<p>But <code>asesam uparujjhati</code> means "fully enclosed".</p>

<p>So in DN11 the guy was asking about place where the physical processes are <em>completely stopped</em> (<em>aparisesā nirujjhanti</em>).</p>

<p>But Buddha said, that's not what we are talking about. It's about "place" where the physical elements have no footing, place inside which all concepts like beautiful, ugly etc., all namarupas, all conceptual discriminations are <strong><em>fully enclosed</em></strong> or fully en-scoped (<em>asesaṃ uparujjhatī</em>).</p>

<p>It is the universal space of information, the universal space of mind, is where they are all enclosed of course. When all discrimination is stopped and this "space" is seen in its original undivided way, is when the unborn/deathless is attained. It is this space is what we in Mahayana call Shunyata. </p>
