With India in a commanding position at 344/3, one can expect Pujara to pile on Lanka's misery and make his 50th test even more memorable on day two.
The lanky off-spinner, who registered his 26th five-wicket haul in his 51st Test, got crucial wickets including that of former captain Angelo Mathews for 26 and Dilruwan Perera for 25.
A few minutes before the stumps, wicketkeeper Wriddhiman Saha took a stunning catch to dismiss Mendis on Pandya's delivery.
Off-spinner Rangana Herath was the most successful among the Sri Lankan bowlers with figures of 4/154.
The resilient Sri Lankan pair of Dimuth Karunaratne and Kusal Mendis displayed their best batting performance to keep India at bay after a first innings debacle guiding the hosts to 209 for 2 here on the third day of the second Test. Kusal Mendis (16*) and Dinesh Chandimal (8*) were at the crease when the umpires made a decision to call it a day at the Sinhalese Sports Club (SSC).
India thumped Sri Lanka in the first Test at Galle by a mammoth 304 runs to lead the three-match Test series by 1-0.
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Upul Tharanga, who made a duck in the first innings, managed two in the second before falling to Umesh Yadav.
Opting to bat first on winning the toss, the Indians were off to a superb start with openers Shikhar Dhawan and Rahul handling the Lankan bowlers quite comfortably.
The opener had been denied his maiden wicket on Thursday after a review from KL Rahul overturned the leg-before wicket decision but a similar review, this time from Chandimal, would not deny Karunaratne his maiden Test scalp. Sri Lanka cricket manager Asanka Gurusinha has now confirmed a grade-one hamstring tear, and said Pradeep would be out of action for a minimum of two weeks. Mendis hit 17 boundaries over the course of his 135-ball innings. However, an injury put him aside for almost two years and he was first noted for his impressive 159 on test comeback against New Zealand. Five balls later, Shami also bowled Rangana Herath (2) with a ideal yorker. Kusal Mendis brought up just his third Test century, while Karunaratne has been supporting him well from the other end.
Having notched a second century in successive matches, Pujara reached close of play 128 not out, alongside Rahane (103 no).