I am a computer science student and am currently doing my Master Thesis in Germany. I am in the second month of the six month duration for the Master Thesis. I wish to pursue a PhD after Masters and I was wondering when the right time is to start applying for PhD positions. I found a few positions that start in September 2015 but I would be done with the Masters only at the end of November. Is it alright to start applying for a position from now itself or should I wait for a few months?
I'd recommend that you start applying a few months before you graduate. The process may easily take several months, and if you want a direct transition, you need to find something before you actually graduate.
In most cases, it will be possible to delay the start of a position by a few months. So by all means, if you find an interesting position that starts a bit before you expect to graduate, you should still apply. Just state the date of you expected graduation (month/year is fine) with your application.
Note that many potential employers, especially if they don't know you from earlier activities, will want to see results of academic work such as a Masters thesis (or at least a draft for it) or other academic texts. If you can't show anything in that direction, it would be good to first focus on positions where you know the professor.
The best time to apply depends on the funding type of your Ph.D. position and on whether the start time is fixed. There are generally two funding types, namely, research assistants (wissenschaftlicher Mitarbeiter) and scholarship based funding.
For research assistants, a master degree certificate is a legal prerequisite to get employed and if the supervisor doesn't know you personally then he probably won't consider your application until a semi-final draft of your thesis is already done. Supervisors can delay the start of their project only if they find an excellent match.
As for scholarship-based positions, you can apply a bit earlier depending on the application deadline. You may even start conditionally without having your master degree certificate issued yet which gives you extra flexibility. Note that issuing the master certificate may take a few months after defending the thesis.