Shikhar Dhawan notched up another test century as India looked set for another big score in the third and final test against Sri Lanka.
Sandakan, Kumara, and Fernando replaced Herath, Pradeep, and Dhanjaya de Silva.
Rahul, who scored his seventh consecutive Test fifty, was the first to go after mistiming a drive to mid-on off Pushpakumara.
Kohli tried to stem the rot during a 84-ball innings, ended when he edged a Sandakan delivery to slip.
It was nonetheless the fastest century by Indian No.8 and the fifth fastest overall by an Indian in Test cricket.
A win in the previous match meant, Kohli is now the only Indian captain to have won two straight Test series in Sri Lanka. Given that India has two quality spinners, Sri Lanka would be hoping to bowl out the visitors as early as possible.
One would be excused for wondering why India's first eleven is even bothering to put themselves through this global net practice session. I know if I can hit a bowler, I go on that basis. The interval was duly pushed back by half an hour, and Pandya went on to dominate an unbroken tenth-wicket stand of 66, racing from 50 off 61 balls to 108 off 93, with the No. 11 Umesh Yadav scoring 3 off 14 in that time.
Dhawan though stayed and scored his second hundred of this series off 107 balls.
Second-game spinner Pushpakumara also wrote himself into the record books, with the 26 he conceded surpassing Suranga Lakmal's mark of 24 (struck by New Zealand's Brendon McCullum in 2014 at Christchurch) for the most expensive Test over in Sri Lanka's history.
Malinda Pushpakumara (18-2-40-3) did not have the greatest of debut Test matches at the SSC, although he did get better the more he bowled, but on day one in Kandy, the left-arm orthodox showed why he has taken bucketloads of wickets in first-class cricket.
The ever dependable Pujara's discomfort at the crease came to an end as he was caught at first slip off Sandakan in the 51st over.
"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".
Contrast this with India, who, even without Ravindra Jadeja, have penetrative spin options in R Ashwin and Kuldeep Yadav, the bubbly 22-year-old chinaman bowler who should play his second Test, and serious depth in quick bowling. Though Dilruwan Perera struggled and was expensive by Test standards, Pushpakumara and Sandakan received plenty of assistance from the dry, grassless pitch.