Journal submission refered to Editor-in-Chief I had submitted to a reputed computer vision journal. Both the reviewers (there were only two) marked it as "reject" with comments that alluded to the fact that they had actually "missed the point". It was interesting that the reviewers missed the point on two major levels, first on the actual aims and scope of that journal and second the actual scope of the conducted research. With 2 reviewers recommending "reject", the Editor decided to "reject" the article.

Even though there was no avenue for rebuttal, I drafted a long email with my rebuttal highlighting where the reviewers had missed the point of my article. The Editor replied saying that he himself was very much surprised by the reviewers decision because from his reading of the paper he actually saw value in it. On top of that, my rebuttal was very convincing. However, he does not feel comfortable reversing the decision because both reviewers had recommended "reject"  hence he is going to refer this to Editor-in-Chief to get his opinion. 

Now, what are my chances of publishing this article of mine with this journal? 

Update: The editor-in-chief got back with a list of possible items for major-revision that they would like to see. The major-revision deadline was quite short (just three weeks), they agreed to postpone the deadline on my request. I tried my best to address the items of major-revision and the article was finally accepted. Perseverance pays! :-)
First of all, your situation is not at all uncommon.  On the contrary, most academics who submit sufficiently many papers find themselves in it from time to time.

The fact that your rebuttal email resulted in an editor's writing back that he saw value in your paper is already worth something: it gives corroboration that your paper has value.  In general it is doubtful that an editor would write that only to be polite, because in doing so he is opening himself and the journal up to further rebuttal from you.  The fact that he is passing your complaint on to the editor-in-chief is further evidence that he takes it seriously.


  Now, what are my chances of publishing this article of mine with this journal? 


If you're asking for a straight-up prediction: that's hard to say.  In general the chance that a paper that gets multiple negative referee reports is eventually published is very small.  However, it is also relatively unusual for an editor to directly communicate disagreement with the referee reports to an author.  The chances depend on how egregiously off-base the referee reports were.  If the editors truly agree that the referees "missed the point on...the actual aims and scope of that journal" then they are going to feel like wronged parties along with you and the chance that they will at least solicit another referee report seems pretty solid.  (On the other hand, if that is the case one wonders why they didn't notice it before you brought it to their attention.)  If a third referee report disagrees wildly with the first two, then perhaps the editors will be inclined to accept the paper (or seek yet further reports).

Nevertheless, unfortunately my guess at the most likely outcome is that the editors will convey their sympathies to you and wish you the best of luck elsewhere.  In my experience editors just do not have enough incentive to overrule referees in this situation.  From a hard-nosed perspective they may be right: if your paper truly is valuable and the referees are wrong, then you can resubmit to another journal of similar quality.  That outcome is in the long run almost as good for you and only detrimental to them if your paper is not just publishable in the journal but outstandingly strong beyond the sort of papers they usually accept.  On the other hand if your paper is flawed and they publish it anyway then they are throwing away all the advantages of peer review.  

In general, it is a rare referee report that doesn't tell you something that could improve your paper.  If a referee wildly misses the point (which again, is not at all uncommon) it is not necessarily your fault...but nevertheless maybe you could rewrite the paper to make it easier to get the point.  Sometimes authors work for months or years on very subtle things and then expect readers to appreciate these subtleties upon a much more casual reading.  The fact that two different referees missed the point still does not imply that their comments have any legitimacy, but it does make it more probable.  If two people miss the point of your work in the same way, then I would certainly take a crack at rewriting the paper to avoid that particular misunderstanding.

All in all, it would be safe to at least start thinking about how you could (perhaps relatively quickly and easily) modify your paper for resubmission.  I would expect the editorial deliberations on this to be rather quick: if you don't hear back from the editors within, say, two weeks, then it would be appropriate to inquire politely on the status of your paper.  I would not advise you to resubmit to the same journal unless you know you'll get new referees: people who have missed the point once are not your best bet for appreciating the new version.