Perera, with a total of 14-under-196, is three shots ahead of Thangaraja, who fired 68.
Gurgaon-based Veer Ahlawat fired the day's best score of seven-under-63 to gain 13 places and finished the day in third position at 10-under-200.
Perera (68-63-65), who was part of the three-way lead at the halfway stage along with Thangaraja and Noida's Vikrant Chopra, fired a second consecutive bogey-free round to break away from the rest of the field.
The tide really began turning the 31-year-old Perera's way when he knocked in a 15-footer for birdie on the 14th to take the outright lead.
Thereafter, it was one-way traffic as Thangaraja three-putted the 16th for bogey and Perera tapped in for another birdie after an unbelievable tee shot on the par-3 17th to build a three-shot cushion.
"I made more regulations today and got a little lucky with the putts on the back-nine. I didn't give the others any chances to catch up with me. I'm delighted to have shot a second successive bogey-free round," Perera said.
Thangaraja (61-70-68) dropped out of the lead for the first time this week after a patchy two-under-68 in round three.
Ahlawat's impressive 63 took him from overnight tied 16th to third, four off the lead, thereby helping him rise into contention.
Defending champion Mukesh Kumar (69) of Mhow, 2017 PGTI Order of Merit champion Shamim Khan (68) of Delhi and Noida-based Vikrant Chopra (70), the joint round two leader, all ended the day in tied fourth at nine-under-201.
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