There was not much to cheer for Sri Lanka in the second session as Pujara completed his half-century on his 50th Test and India went into tea at 238 for three.
Chandimal's return will be a huge boost for the Lankans, who suffered a 304-run thrashing at the hands of the visitors in the first Test, at the Galle International Stadium, last week.
Thirimanne has been out of the Test team for more than a year and has also not featured in the traditional format since playing against England in June 2016.
India, who can clinch the three-Test series in Colombo, were 101 for one at lunch after winning the toss and choosing to bat.
For the second time in the series, Virat Kohli won the toss and had absolutely no hesitation to bat first, and, while there was one brief moment, at 133/3 when Sri Lanka looked like they might claw their way back and make things hard for India, it vanished pretty quickly as Cheteshwar Pujara and Ajinkya Rahane struck up a delightful partnership for the fourth wicket.
Shikhar Dhawan was out after his typically aggressive 35 off 37 deliveries contained five boundaries and a six.
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India have made one change to their playing bringing in fit-again KL Rahul in place of Abhinav Mukund.
"Obviously KL has been our established opener".
Dhawan, who had narrowly missed out on the maiden double century of his career in the first Test, seemed to be in excellent form here as well.
It was the No.3's third hundred in his past four Tests, after he was a dominant figure in India's epic 2-1 series triumph over Australia in February-March, highlighted by a classic 202 in the third Test in Ranchi.
India were without both their first choice openers in Galle with Murali Vijay also unavailable due to injury.
Sri Lanka were likely to debut left-arm spinner Malinda Pushpakumara to partner veteran Rangana Herath, Chandimal said. This is probably course-correction, and an attempt to make sure that Sri Lanka has at least a fighting chance, even though India has the top two Test bowlers as per the ICC rankings in the spin combine of Ravindra Jadeja and R Ashwin.
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