Is it possible to get into IIT Tirupati just by the GATE qualifying marks?

Yes, it may be possible. Here are the reasons why-

1. IIT Tirupati is a very new IIT, established in 2015.
2. It is not well known currently, especially in North India. 
3. It releases its applications quite early.
4. Its MS and Phd. batches started only a few years ago, so those with better scores will prefer NITs over IIT Tirupati.
5. The cutoff for MS is also low in IIT Madras because very few students are interested in pursuing the course.

Ultimately, the number of applicants and the interview round will decide your fate.