Brief scores: South Africa 335 all out in 113.5 overs (Markram 94, Du Plessis 63, Amla 82; Ashwin 4/13, Ishant 3/46).
Openers Murali Vijay (four) and Lokesh Rahul will resume in the afternoon on a slow wicket that is uncharacteristic of the venue, but will provide bounce and is likely to quicken up over the next two days.
Kohli strode in with India under pressure at 28-2 after losing two wickets in two balls.
South Africa profited with what could be crucial first innings runs through this period, before Rabada was superbly caught by, ironically, Pandya at deep mid-wicket as he attempted a hook off the excellent Ishant Sharma (3-46). South Africa were 148-2, still looking good, as AB de Villiers walked in. The step across brought him closer to the line of short balls outside off, and he picked up a square-cut boundary off Vernon Philander in this manner, and the shuffle also prompted South Africa to aim for his pads, which allowed him to pick up runs on the leg side every now and then. His departure after another 51-run stand would mark the beginning of a drastic change in Saturday's proceedings, one that would put India in the driver's seat by the time umpires called it a day.
The South African batsmen took a bit of momentum out of those two misses, with Du Plessis turning up the aggression as the hosts surged past 300.
Overnight batsman Keshav Maharaj (18) was showed route to the pavilion by Indian seamer Mohammed Shami.
Kagiso Rabada (11) then hung around for nearly 12 overs with Du Plessis, adding 42 for the eighth wicket.
At the other end, R Ashwin looked like getting Rabada out at any moment, confounding the left-hander with his dip and turn.
Pandya, replacing Shami, found Rabada's edge in his first over but the ball didn't carry to first slip; an argument could be made that the wicketkeeper Parthiv Patel should have dived across and gone for the catch. After the defeat in the first Test match, the Indian skipper replied that they chose to go in with players who are now in a better form and comfortable mindset to battle out the tough conditions in the African continent.