Bad light forced the umpires to take the players off the field about 20 minutes into the day's last session. With the light not improving, play was called off for the day half an hour later.
The Proteas' batsmen struggled in the limited passage of play possible. Indian pacers Umesh Yadav and Mohammed Shami effectively used short deliveries with good pace to take a wicket apiece.
Shami got rid of Dean Elgar (0), while Yadav dismissed Quinton de Kock (4) to rattle the touring side.
At stumps, Zubayr Hamsa (0 not out) and Faf du Plessis (1 not out) were at the crease, trailing by 488 runs.
This was after India declared their first innings at 497-9. Rohit Sharma scored 212, his highest test score and a maiden double hundred to put the hosts in command.
Sharma faced 255 deliveries, and hit 28 fours as well as six sixes. He and Ajinkya Rahane put on a record fourth-wicket stand of 267 runs. Rahane scored 115, his 11th test hundred and a first on home soil since 2016.
India had resuming at 224-3 after bad light stopped play on Saturday as well.
Sharma and Rahane set a hectic pace of scoring in the morning session making 60 runs in the first hour.
Rahane reached his 11th test hundred off 169 deliveries in a free-flowing innings, which included 17 fours and a six.
Debutant left-arm wrist spinner George Linde (1-58) eventually broke the partnership having Rahane caught behind in the 76th over. The duo added 267 runs for the fourth wicket, a record for India against South Africa in test cricket.
Sharma, though, continued his dominance of the visitors' attack and not long after passed his previous best test score of 177 against the West Indies at Kolkata in 2013.
Post lunch, Sharma added 64 runs for the fifth wicket with Ravindra Jadeja, who also scored his 13th test half-century.
Sharma got to his double hundred with a six. He looked to be in an attacking mood thereafter but pulled Kagiso Rabada (3-85) straight to fine leg in a bid to up the ante.
Playing his 30th test, Sharma is the first Indian batsman to accumulate 500-plus runs in a test series against South Africa. The previous best was 388 runs by Mohammad Azharuddin in 1996-97.
After Sharma's dismissal, Jadeja took the innings forward. He added 47 runs with Wriddhiman Saha (24) and another 33 runs with Ravichandran Ashwin (14).
With the threat of another thunderstorm looming, the Indian batsmen piled on the misery for the South African bowlers.
Jadeja was dismissed off George Linde, with the debutant wrist spinner finishing with figures of 4-133.
Umesh Yadav was the last wicket to fall, but not before he smashed five sixes and scored 31 off only 10 deliveries.
On day one, bad light halted play as Sharma's third century in this series helped India recover from a precarious 39-3.
India took an insurmountable 2-0 lead in the three-match series after winning the first two tests in Visakhapatnam and Pune.