Saaniya's round has been the only sub-par round of the week at the challenging Hyderabad Golf Association course.
After a first round 76, she is now one-over 145 and leads by two shots over Amandeep Drall (73).
Seasoned Smriti Mehra (74) was third, while Gursimar Badwal (79), winner of the last two events, fell back as she dropped five shots between ninth and 12th holes.
Chandigarh pro Saaniya skipped the last two events in Bengaluru as she played at the LPGA Qualifying Round Stage I in US. She last won in Coimbatore in 2015.
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Today she bogeyed the third and fourth, but then went on a birdie streak from the sixth hole. She had four birdies in a row and turned in two-under 33.
On the back nine, a bogey on 11th was neutralised by a birdie on 15th and she finished at 69, by far the best score this week.
Amandeep Drall who had a tough run between fifth and ninth holes, during which she dropped four bogeys, also had a bogey on par-5 17th and ended at 73.
She dropped a double bogey and two bogeys during the stretch and is now third at 148.
Gursimar was just not able to find her rhythm as she had just one birdie against seven bogeys and one double on a rather disappointing day.
For the second day running, Trisha Sunil and Ayesha Kapur carded identical rounds of 79 and were tied-6th at 155, while Afshan Fatima (77) and Siddhi Kapoor (81) were tied-8th at 156.
On the final day, Saaniya, Amandeep and Smriti will go out in the leader group.
Only Amandeep has tasted victory this season as she won twice in Ahmedabad and Gurgaon legs, while Smriti's best this year has been second at Ahmedabad and Saaniya's best has been second at Kolkata.