Kohli scored 112 off 119 balls with the help of 10 boundaries and put on 189-run stand for the third-wicket with Ajinkya Rahane (79 runs of 86 balls) as India chased down the target of 270 with 4.3 overs to spare.
India beat South Africa by six wickets in the first ODI to go up 1-0 in the six-match series at Kingsmead in Durban.
Markram, 23, will bat at number four for de Villiers who has been ruled out of the first three ODIs due to a finger injury.
The mega player auctions of the IPL will be held on February 27 and 28 in Bengaluru, the last two days of the third and final Test between India and South Africa.
South Africa have managed to build important partnerships - du Plessis and de Villiers putting on 114 runs in the 1st innings in Cape Town, and then De Villiers and Elgar stitching 141 in the 2nd innings at Centurion Test - which made the difference.
Watch Live Cricket Streaming Online India vs South Africa Third (III) Test day 4 Cricket Match Ball by Ball Commentary, Ind vs SA Cricket Score Live Updates on Sony Sports through our Live Blog at India TV
Meanwhile, South Africa have already sealed the three-match series, after winning the first Test in Cape Town by 72 runs and the second Test in Centurion by 135 runs.
The Proteas' skipper also expressed concerns about the Centurion pitch and compared it to the raging turners in the 2015 series in the sub-continent conditions.
If South Africa commit another minor over-rate breach in a Test within 12 months of this offence with du Plessis as captain, it will be deemed a second offence by du Plessis and he will face a suspension.
According to South Africa skipper Faf du Plessis, the hosts were pretty much on top of India in all five days of the game.
Debutant Lungi Ngidi emerged as the newest fast-bowling nemesis that India discovered as he snared six scalps for a mere 39 runs. He replaced injured pacer Dale Steyn in the second Test.
Take a look at some of the highlights that went down on day four of the second Test at Centurion between India and South Africa.
Morkel said the game will have an outcome despite the loss of time today due to rain and bad light.
Kohli held together India's innings with a classy unbeaten 85 off 130 balls along with all-rounder Hardik Pandya (11 not out) at the crease. India reached 183/5 in 61 overs in their first innings at stumps in reply to South Africa's 335 all out.
Cricket Live Score India vs South Africa: Watch Ind vs SA Cricket Live Streaming Online and Get Cricket Live Score ball by ball Updates India Vs South Africa 2nd Test Match Day 2 in Centurion through our live blog at India TV.
India's record of nine consecutive series victories will be on the line from Saturday after the hosts took a 1-0 lead in the three-match series in Cape Town.
Faf du Plessis kissed on Kagiso Rabada’s forehead after the pacer took the wicket of Hardik Pandya in the first innings of Cape Town Test.
Steyn drew a massive applause from spectators for each of his blocks during his five-minute unbeaten stay at the crease on day four of the Cape Town Test against India on Monday.
Du Plessis further said that they would have liked a total of 350 runs as the 208-run target made the hosts nervous at lunchtime on day four of the Cape Town Test.
South Africa beat top-ranked India by 72 runs in the first Test on Monday, forcing out the best side in the world for just 135 on the fourth day at Newlands in Cape Town on Monday.
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