The main highlight of South Africa’s second innings was of AB de Villiers and Dean Elgar, scoring 80 and 61 respectively.
"It's massive for us and I think it's massive for India, knowing he's not batting," said South Africa opener Dean Elgar.
"He's a very special batsman, as we saw in the first innings. I'm sitting here with a smile on my face because he's one less very competitive, extremely talented batsman we have to deal with," he added.
A few big moments in the last two overs. First snicko picked up an edge that SA did no appeal for when Pujara was facing up to Morkel. Then there's a huge appeal for Ngidi against Patel. SA opt to rightly not review. India 28/3 #ProteaFire#SAvINDpic.twitter.com/cnAZ2mY1x8
The Proteas managed to set India a mammoth target of 287 at the Centurion.
For India, apart from Mohammed Shami, Jasprit Bumrah took three wickets and Ishant Sharma also managed to get two.
Shami had struck three times for his team to dismiss two set batsman AB de Villiers and Dean Elgar and one new batsman Quinton de Kock in quick succession.
Skipper Faf du Plessis and Vernon Philander were the two batsmen on the crease who generated a partnership to take South Africa's score to 173/5 at lunch.
Earlier on Day 3, Kohli hit a masterly 153 in India`s first innings of 307 to stay in touch in Centurion, even though South Africa stretched 28-run first innings lead to 118 by scoring 90 for two in their second spell at-bat on a storm-shortened afternoon.