Sri Lanka's slide, after facing a mere 18 overs, happened after Pujara (145 not out) guided his side to 312 all out (100.1 overs) in the first innings. Pujara became the 45th batsman in Test cricket to carry his bat through an innings.
The hosts were in trouble very quickly as they tried to negotiate nearly an hour's play before lunch.
Ishant Sharma (2-12) and Umesh Yadav (1-20) exploited the still-fresh pitch and put the new Kookaburra ball to good effect.
The former could have had a wicket in the first over itself, when he induced an edge off Upul Tharanga on 0, but KL Rahul dived in front of first slip and dropped the catch.
The two pacers continued to bowl well and beat the batsmen on umpteen occasions, but that one chance wasn't coming.
It finally did in the fifth over, when Tharanga (4) edged once again and this time Rahul didn't make any mistake. There was a slight doubt of a no ball but the decision went in the bowler's favour.
In the next over, Yadav bowled Kaushal Silva (3), the opener dragging a short ball onto his stumps. Dinesh Chandimal (23) came out to bat at number four then and played some attacking shots.
He wasn't fazed by the Indian bowling and hit five quick boundaries off the 27 balls he faced. But just when it looked he was set to play a counter-attacking innings like in Galle, he was adjudged LBW to Stuart Binny (2-14) in the 12th over.
The ball hit him high on the back-thigh and it was a poor decision from umpire Rod Tucker as the delivery looked to be carrying over stumps.
The misery continued for Lanka thereafter as skipper Angelo Mathews (1) was caught behind off Ishant in the 17th over. Binny took his second wicket in the next over, Dimuth Karunaratne (11) edging to second slip as Rahul took a comfortable catch.
Earlier, Pujara became the fourth Indian batsman to carry his bat through after Sunil Gavaskar (in 1983 at Faisalabad vs Pakistan), Virender Sehwag (in 2001 at Galle vs Sri Lanka) and Rahul Dravid (in 2011 at the Oval vs England).
India's first innings came to an end in the seventh over of the day. Starting at their overnight score of 292/8, the visitors were able to add 20 runs before they were bowled out. Ishant Sharma (6) was bowled by Rangana Herath (3-84) on the 9th delivery of the morning, the tail-ender looking to go big but completely missing the line.
Four overs later, he also bowled Umesh Yadav (4) while India crossed their 300-mark in the 98th over. Dhammika Prasad (4-100) finished as Lanka's best bowler on display, while Nuwan Pradeep (1-52), Angelo Mathews (1-24) and Tharindu Kaushal (1-45) also took a wicket each.
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