Will a dishonesty incident destroy the chances of getting into a good PhD program?
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.