Pandya finally succumbed to spinner Lakshan Sandakan on the third ball of the second session as India's innings ended without adding to the lunch total.
Earlier, as the day began, Pandya and Wriddhiman Saha (16) looked to bat for time in a bid to resurrect India's floundering first innings. Cheteshwar Pujara led from the front in last two Test matches alongside Shikhar Dhawan and Abhinav Mukund who are determined in the opening job. Kohli would be hoping India do not lose a wicket in the first one hour on day 2.
Dhawan though stayed and scored his second hundred of this series off 107 balls. India's only concern coming into the Test was Kohli's atrocious form in Test cricket, something that seems to have been exacerbated by his captaincy.
"If it's consistent it's going to be good going ahead because players will be more aware of how they need to conduct themselves on the field and it'll only help the game get better", the skipper told reporters.
Pushpakumara broke the big partnership of the two India openers, with Rahul chipping a ball to Dimuth Karunaratne, who took a nice catch on the jump at mid-on. Dhawan went on get a ton.
A return to the attack with a slightly older ball made no difference to Kumara's fortunes - he went too full, rather than too short, in his first over back, and both Rahul and Dhawan drove him for fours.
Kohli and Rahane were then tasked with stabilizing the innings, which they did, ensuring no more wickets were lost as the team headed into Tea. Asked if the team is looking forward to that record, Kohli said: "For us it's just about playing another Test match and trying to win another Test match".
Saha and Pandya will resume India battle, Saha is fairly set but Hardik is quite new to the crease.
"The Sri Lanka bowlers bowled well and pulled the match a little bit on their side", Dhawan, who celebrated his sixth Test century, said.
For Sri Lanka, Pushpakumara scalped 3 wickets, while Sandakan took 2 wickets and Fernando one.
With India also picking chinaman Kuldeep Yadav in place of the suspended Ravindra Jadeja, this was the first Test match since January 2004 - when West Indies' Dave Mohammed and South Africa's Paul Adams featured in Cape Town - to include two specialist chinaman bowlers. Though Dilruwan Perera struggled and was expensive by Test standards, Pushpakumara and Sandakan received plenty of assistance from the dry, grassless pitch.