Yeah! You will be eligible for the stipend. The eligibility of the stipend is that the student have to get admitted with in the validity of the GPAT score. So Don't worry.

In M.Pharm you will receive an stipend/ scholarship of Rs.12,500(approx). This amount is entirely dependent if you qualify and gets admission on the basis of GPAT score in any of the three validity years and doesn't depend on B.Pharm / 10+2 aggregate percentage.

I hope this answer helps. All the very best for your future endeavors!