Resuming the final session at 235/3, left-arm spinner Pushpakumara scalped the wicket of Rahane before Sandakan sent Kohli back into the hut just when the skipper was looking good with three fours.
India won the toss and opted to bat first once again.
In the fourth over of the second session, the pair went past the 150-run stand and soon held the record for the highest opening stand against Sri Lanka in their own backyard when they reached 175.
Reportedly, both Jadeja and Ashwin might be rested for the upcoming limited-overs series against Sri Lanka.
He put on only 10 runs with Kohli as India were left to rebuild their innings despite being in a comfortable position.
Because MS Dhoni doesn't play Test cricket, he was called to prove his fitness at National Cricket Academy (NCA) in Bengaluru along with teammate Kedar Jadhav, Suresh Raina, Yuvraj Singh, Jasprit Bumrah and other probable candidates for the limited-overs series.
"I was saying jokingly that if you bat like a king, you should also get out like a king, you should not be dismissed like a soldier". Specially once we got out, the way he came back and bowled, it was nice for them.
Dhawan faced 123 balls in his knock and punished the home bowlers with 17 boundaries.
Besides Pujara, Rahane too looked uncomfortable against the spinners, unable to judge the ball.
It is not easy because everyone wants to play and luckily we have such players who are just waiting for opportunities. Read Also Umesh Yadav reveals he would struggle to control leather ball early in his career, credits coaches for honing his skills Cheteshwar Pujara leads India's run-scorers with two centuries and an average of more than 100 in India's three innings so far. Kohli batting on 42, lost his concentration and finally succumbed to a bowl pitched wide outside off to play a shot which he avoided for the most part of his 42 run inning - the drive, edging it to slip.
Pallekele: Sri Lanka skipper Dinesh Chandimal has said he is hoping to avoid a 0-3 series whitewash against India with assistance from a lively pitch and a young fast bowling attack.
With Kuldeep and Sandakan featuring in the match, it was only the second time since 2004 when two "chinamen" bowlers featured in the same game after Dave Mohammed (West Indies) and Paul Adams (South Africa) at Cape Town.
The former then fell immediately afterwards caught behind off Sandakan.