Playing his first match as test captain at his home ground, Kohli partnered Ajinkya Rahane (52 not out) to cobble together the first century stand of the low-scoring series after India had slumped to 57-4 following Morne Morkel's triple strikes.
The duo had raised 133 runs for the fifth wicket when bad light stopped play.
India's overall lead swelled to 403 against a beleaguered South African team who were shot out for 121 in the first innings and have not gone past 185 in the series.
"We batted well in the first innings, they folded cheaply. I think 213 is a big margin," India all-rounder Ravindra Jadeja told reporters, referring to the hosts' first innings lead.
"As the match progresses, this wicket is going to deteriorate. We are in a strong position."
Morkel orchestrated India's top order collapse, claiming two wickets in two balls in the morning after India, who have taken an unassailable 2-0 lead in the series, had opted against enforcing the follow-on and decided to set the visitors a target instead.
Morkel drew first blood with a short delivery to dismiss opener Murali Vijay caught behind. The batsman pointed to his arm-guard to suggest he did not nick it before leaving the field shaking his head.
Rohit Sharma was sent ahead of Cheteshwar Pujara, who was hit on the arm while fielding at short leg on Friday, but the batsman could not justify his promotion.
The right-hander, who scored one in the first innings, was out for a golden duck after a fuller Morkel delivery eluded his tentative prod and rearranged his stumps.
After the lunch break, Morkel castled Shikhar Dhawan with a searing, inswinging yorker to dismiss him for 21 while Imran Tahir dismissed Pujara (28).
India could have been in bigger trouble when Kohli, then on five, was ruled caught behind only to be called back after TV replays showed the leg-spinner had overstepped.
Kohli, hand on hip, was seen glaring at the umpire after being given out initially suggesting he did not nick it in an act of defiance that is unlikely to go unnoticed by the match officials.
That was the only blip in an otherwise fluent knock by the Indian captain whose silken touch was in full display in each of the 10 boundaries he hit in his knock.
He and Rahane were largely unperturbed during the series-high partnership even though Morkel bowled his heart out, mixing pace and reverse swing but not getting much support from the other end.
"We threw everything at them this morning, but they batted incredibly well," said Proteas paceman Kyle Abbott who did not mind India batting on further.
"To be quite honest, the longer they bat, probably the happier we are because more overs are taken out of the game.
"To be quite honest, I thought they'd probably have a crack at us tonight, maybe the last hour or so. But they want to drag it out."
(Editing by Sudipto Ganguly)
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