Dipankar Kaushal of Noida was in third place having posted a three-under-67.
While Saini fired a bogey-free 66, Baisoya's round featured six birdies and two bogeys.
Saini said, "I was in brilliant putting form today as I sank birdie putts from 20 and 15 feet on the 10th and third respectively. I also created some birdie opportunities with my hitting.
Baisoya, who played alongside Saini on the amateur circuit till last year, said, "The top-10 finish in Nepal couple of weeks back has helped me raise my game. My putter was hot on the front-nine today as I sank birdie putts from 10 feet on the first and fifth. I also hit it really well.
"I landed my tee shot within five feet for birdie on the fourth. I narrowly missed out on eagle opportunities on the 12th and 18th where I eventually bagged birdies."
Jaipur's Vishal Singh is in tied fourth along with Gurgaon's Arshpreet Thind and Richard Stephen Hilton of Dehradun at two-under-68.
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