Perera and Vikrant Chopra fired scores of seven-under-63 and five-under-65 respectively to move into the joint lead with the overnight leader, Sri Lanka's Thangaraja (70) at nine-under-131.
Defending champion Mukesh Kumar of Mhow posted a four-under-66 to lie one shot off the lead in fourth place at eight-under-132.
Perera (68-63), who was tied 12th, seven shots behind the leader, after round one, worked his way up to the top with the day's best score, a flawless round that featured seven birdies.
His birdies on the 11th and 14th were a result of two 15-feet conversions.
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"The good birdie putts at the start gave me a lot of confidence as prior to this week I had struggled with my putting," Perera, an Asian Tour regular, said.
Chopra (66-65), who was overnight tied third and five off the lead, came into contention with a classy effort of 65 today.
Thangaraja (61-70), who had shot a course record equalling 61 for a three-shot lead in round one, conceded his sole lead after posting a quiet 70.
The only Tamil Nadu-based golfer to make the cut was rookie Shivnaren Srinivasan (70-69).
Chennai-based Srinivasan was tied 25th at one-under-139.
Fifty-eight professionals made the cut that fell at three-over-143.
Mumbai's Anil Bajrang Mane, who made a hole-in-one on the 17th during his second round of 71, made the cut by one shot as he totalled three-over-143.
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