Cheteshwar Pujara and Ajinkya Rahane hit centuries as India took opening day honours on 344-3 at stumps against Sri Lanka in the second Test in Colombo on Thursday.

Pujara (128) and Rahane (103) put on an unbeaten 211-run partnership for the fourth wicket to thwart Sri Lankan bowlers who struck two crucial blows in the afternoon session.

The in-form Pujara registered his 13th Test century in his landmark 50th game as Rahane fired his ninth Test hundred.

The visitors, who lead the three-match series 1-0, wobbled slightly when Lokesh Rahul went for 57 and skipper Virat Kohli followed for 13 soon after lunch.

Rahul, who scored his eighth Test fifty despite only just recovering from a virus, was run out in a mix-up with Pujara.

"I was disappointed because I have been away from the game so long and I didn't want to get out at all," he told reporters at the Sinhalese Sports Club (SSC) Ground.

He said knowing the team was waiting for his return post recovery "made a big difference and I came back with a lot more confidence".

"The pitch was on the slower side and would turn as the Test went on," he added.

Veteran left-arm spinner spinner Rangana Herath sent Kohli trudging back to the pavilion with a tossed-up delivery that got the edge of the captain's bat and went to slip.

Pujara and Rahane ground out the runs to deny Dinesh Chandimal's side any more wickets during the day.

Pujara, who scored 153 in the first innings of the opening Test, hit 10 fours and a six.

Rahane also tackled the spinners with aplomb, using his feet to great effect during his 168-ball stay at the crease so far.

Sri Lanka's interim coach Nic Pothas praised Rahane for his gritty knock but conceded the squad didn't maintain pressure on the world's top Test team.

"Rahane came and played very well. From that point onwards we didn't perhaps execute as well as we had done up to that point," said the former South Africa player.

"We just released the pressure a little bit. That was the turning session. India got momentum back. This is the day one and it's Test match cricket. It's about how you bounce back."

In the morning session, off-spinner Dilruwan Perera had Shikhar Dhawan trapped lbw for 35 after the tourists elected to bat first.

Debutant left-arm spinner Malinda Pushpakumara was still searching for his first Test scalp as paceman Nuwan Pradeep had to leave the field due to a suspected pulled hamstring.

The hosts need at least a draw to stay alive in the series.