What are my chances of being accepted in a Ph.D. program with poor M.Sc. grades?
You need to talk with your thesis supervisor to find out whether the department's regulations are "hard" or "soft."  Many departments have clear regulations which are "soft" in the sense that they can have small exceptions made if a professor can make a case for why such an exception should be made.  This is very often the case, and if this is the case for your department and your supervisor wants you as a Ph.D. student, then you are fine.

Sometimes, however, a department will not allow such leniency for its professors.  If this is the case, and your supervisor wants you as a Ph.D. student, then they should also be able to advise you on what to do to try to get yourself into compliance with the regulations.