Does having an article retracted due to professor's ethical misconduct mean my career is over?
If I understand your description, there is no finding of academic misconduct against you.  You have co-authorship of a retracted article, where the problem appears to have been caused by the misconduct of your co-author, and unbeknownst to you.  The incident occurred when you were only a masters student acting under the direction of a professor.  If this description is accurate, I do not see why this matter would affect your future research career.  I cannot imagine this being held against you by a selection panel for PhD candidature, or later in your career.

To ensure you have evidence confirming your account of events, I would strongly recommend asking the university to give you a formal written finding describing the matter and confirming that you did not commit academic misconduct.  You should also ask them for a letter of reference that gives an account of your abilities, with an apology to you for misconduct of this professor.  Bear in mind that the university employed the professor that instructed you in this matter, so they bear some responsibility to you here, and you have some good leverage to get them to give you a formal exoneration.  If you have trouble getting them to give you this, I would recommend speaking to a solicitor to look at your options.  By taking you on as a student the university had a responsibility to you, and it is responsible if its employee harms your research work through his misconduct.

The academic journal has no corresponding obligation to you, so what I would recommend here is to get your formal exoneration letter from the university and then send it to the journal.  Ask them to append a description to their retraction (the online version) noting that you were not responsible for any misconduct in this matter.