Virat Kohli led by example with a batting masterclass as India stayed in contention on the third day of the second Test against South Africa at SuperSport Park on Monday.

Captain Kohli hit a masterly 153 in India's first innings of 307 to stay in touch in Centurion, even though South Africa stretched a 28-run first-innings lead to 118 by scoring 90 for two in their second batting effort on a storm-shortened afternoon.

India are slightly behind going into day four despite Kohli's innings and two early wickets from opening bowler Jasprit Bumrah, but they could justifiably feel that they were still in with a chance of levelling the three-match series following South Africa's 72-run win in the first Test at Cape Town.

"Virat's innings was very crucial for us. The game is in the balance and we will look to create pressure and take early wickets tomorrow," said Bumrah.

But Kohli was clearly not happy when play resumed in South Africa's second innings after an hour-long rain break.

He was seen in conversation with the umpires, which Bumrah said was about the condition of the ball.

"The ball was swinging (before the break) but when we went back, both sides of the ball got wet so the ball stopped swinging," added Bumrah. "We asked what can we do to get the ball dry."

- Breathtaking strokeplay -

Kohli had lamented India's poor batting in Cape Town and he could not have provided a better demonstration of how to handle South Africa's four-pronged pace attack.

In a model of concentration, good judgement and occasional breathtaking strokes, Kohli batted for 380 minutes, faced 217 balls and hit 15 fours.

It was his 21st Test century to go along with 15 half-centuries, the best conversion rate since Don Bradman of any batsman who has passed 50 more than 30 times.

He was last man out when he was caught in the deep off Morne Morkel, hitting to one of eight fielders on the boundary as he tried to squeeze some extra runs with his tailenders.

Morkel finished with four for 60, taking the last three wickets.

But he also felt a little disgruntled, saying the pitch was reminiscent of those usually found in India.

"I've played cricket here all my life and never seen a wicket like this," said Morkel.

"It was really hard work in the heat with conditions really, really tough."

Despite his lamentations about the conditions, Morkel said there was a good chance of South Africa clinching the series.

"Even if we got 250 ahead it would be tough to get on the last day, with the wicket turning a bit and the ball keeping low."

Kohli received minimal support from his team-mates, with Murali Vijay (46) and Ravichandran Ashwin (38) the only other batsmen to reach 20.

Ashwin helped Kohli add 71 off 87 balls for the seventh wicket but he lived dangerously after being peppered by short-pitched balls from Kagiso Rabada at the start of his innings.

South Africa's second innings got off to a poor start as Bumrah reduced them to three for two.

Aiden Markram was Bumrah's first victim, falling leg before wicket as he played back to a ball which cut back and kept low. Bumrah followed up with the wicket of Hashim Amla, who was also trapped on the back foot by a similar delivery.

Both batsmen were so palpably in front of their stumps that neither sought a review.

India had opened the bowling with off-spinner Ashwin and he troubled left-handed opener Dean Elgar. But Elgar survived to share an unbroken 87-run partnership with AB de Villiers, who batted confidently to reach 50 not out. Elgar was unbeaten on 36.

A thunderstorm interrupted play for an hour when South Africa were 68 for two. It resumed for another 27 minutes under gloomy skies with the floodlights on before bad light ended the day.

Both batsmen survived some anxious moments, in particular Elgar, who on 29 edged Bumrah at catchable height between wicketkeeper Parthiv Patel and first slip Pujara.