Did you get your degree outside Germany? If so, you should check in the Anabin database [1] whether your degree is properly recognized in Germany. If it isn't, you'll need to figure out a way to convince the University that your degree is valid. Your future PhD advisor can guide you through this - the procedure often involves sending enough proof to a committee that will then say "yes, this is acceptable".
If your degree is recognized, then you should explain in your cover letter that you have a non-thesis Masters. A paragraph about the extra work you had to do instead would be nice. If/once you make it to the interview, I would expect to be asked a couple questions about this.