Will a dishonesty incident destroy the chances of getting into a good PhD program? This is going to be a long post but I believe is the only way to understand my situation.

I studied B.Sc in Information Systems Engineering in a small private university in Latin America, it's not a research oriented institution and thus does not have a high reputation, especially outside my country. My GPA is very high (here grades range from 0 to 100; I have a 84.5 GPA which is top 12~15% of the class).

After having completed my first degree I wanted to study M.Sc in Computer Science, in a different university, much larger and public-founded, that has a relatively good reputation worldwide(ranks consistently among top 300 universities in the world).

To get into the program I was asked to complete some supplementary courses and get a certain minimum grade average. On my first semester I got good grades BUT I ran into some serious trouble in one final exam.

In this final exam, I fell asleep and arrived a few minutes after the exam had started, with all the hurry and all I forgot to take my phone out of my pocket (It's forbidden to have a phone on you during test). One of the exam supervisors noticed it and I was found guilty of academic dishonesty (which meant I had no chances of continuing towards this degree). I was pissed off but instead of quitting, i pursued another degree, in the same university but in a different faculty. I pursued M.Sc in Information Systems Engineering.

To be able to get into this new program, I was asked again to complete some supplementary courses, this time I got excellent grades and didn't run into any problems. Now I'm about to start my first semester in the M.Sc, and I started to think about PhD.

So finally I can ask the question: will this incident affect my chances of getting into a good PhD program? I mean if I wanted to go abroad say to study in the US, will this incident hurt my chances beyond repair?

Edit: Possibly a new issue has arised. I started to worry about being rejected from this M.Sc., even if I completed all the sumplementary courses with grades higher than requested? 

After this incident had ocurred and after the discipline hearing in which I got "disqualified" instead of the actual grade as punishment, I applied to this different M.Sc program at the same University. 

I did send an email to one professor that is in the acceptance comitte of this different Masters program, asking about my chances of getting into the Masters(I didn't mention this incident, I just asked if I stood a chance). 

He replied with the list of supplementary courses but now that I think about it, he probably didn't even look at the current transcript of the university, He probably just look over the transcripts of the B.Sc. 

I mean I have with me a letter (which I received after the hearing) that says: You have to complete all these courses with minimum GPA of X, which I did, and every grade has to be no less than Y, which I also did.

Should I be worried?
A citation of exam disqualification on your official transcript will probably arouse some concern in those who see it.  (FYI, although most or all graduate programs will ask for your undergraduate transcripts, it is not guaranteed that a given admissions committee will read them carefully enough to catch this.)  

Switching into a different master's program at the same university is a good idea.  If you succeed in doing that, then the issue was clearly not of the highest level of seriousness, i.e., not serious enough to get you kicked out of the university.  Assuming you can switch, Captain Obvious has just told me to inform you that you should keep your nose absolutely clean (and leave your cell phone at home!) for the remainder of your new master's program.  Also I would put more than the normal effort in to make sure you get the best possible grades.  

Now what happens when you apply for a PhD program elsewhere, e.g. at a good American university?  Assuming that the disqualification will continue to appear on your transcript, in my opinion you should address this in your personal statement and also ask a sympathetic faculty member to confirm your story in their letter.  The tone here is very important (and it is also important that you do not dwell on the issue too much; more than one paragraph would probably be excessive).  If this is handled well then it becomes somewhat in the eye of the beholder how seriously to regard the issue.  

For my part, assuming I believe the story you've told I have a lot of sympathy for you: forgetting to remove your cell phone from your pocket is a failure to comply with an exam directive.  I am a mathematician so can be very literal-minded, but I think that to call something "academic dishonesty" there must be some actual dishonesty involved, i.e., an attempt to cheat, deceive or take unfair advantage. [This means that plagiarism can be separate from academic dishonesty, which is a fine cutting but I think correct.  Also plagiarism has a victimized party, an important distinction.]  So to me calling your action "academic dishonesty" seems extreme and unkind. 

This is also colored by the fact that in my academic culture (public university, US) we would generally not ask students to remove items from their own person before taking an exam nor would we feel comfortable searching a student's person in an exam situation.  It may be that in your own culture the removal of cell phones upon taking an exam is so standardized that the failure to do it looks self-servingly negligent.  Still, for me it is not a big problem.  As an example, when I give exams in freshman calculus, calculators are not permitted.  Once I noticed 5-10 minutes into an exam that a student was in fact using a calculator.  I walked over to him, pointed out where it said on the exam sheet that calculators were not permitted, asked him to put away his calculator, took away the work he had done on the exam so far and allowed him to start fresh.  I thought it was an honest mistake which gained him little if any advantage and I didn't see the point in making a big stink about it.  Others might feel differently.  

In fact, "Others might feel differently" is one of my main points: I think that you should apply to a larger number of programs than you otherwise would because some programs and people will find this problematic and others likely will not, in a way that will not be possible for you to predict in advance.  

Anyway, good luck and remember that cell phones are the root of all evil.