After being bowled out for 55 in the first innings, South Africa were 62 for three in the second innings at the close, still 36 runs short of India’s first innings total of 153.
Mohammed Siraj produced a sensational career-best spell of six for 15 as South Africa were bowled out before lunch after choosing to bat first on a pitch which gave considerable help to the fast bowlers throughout the day.
South Africa's total was their lowest in almost 92 years, since they were bowled out for 36 and 45 by Australia on a rain-affected pitch in Melbourne in February 1932.
It was the lowest total by any team in a Test against India, beating 62 by New Zealand in Mumbai in December 2021.
Siraj bowled superbly in an unchanged nine-over spell.
India cruised into the lead in 9.4 overs, before the afternoon drinks break.
The tourists seemed set for a substantial advantage when they reached 153 for four, with the experienced Virat Kohli and KL Rahul at the crease.
But the remaining six wickets fell for no runs in 11 balls.
Lungi Ngidi had Rahul caught behind and took two more wickets in the same over.
Kagiso Rabada had Kohli caught at second slip for 46 in the next over, Mohammed Siraj was run out and Prasidh Kumar caught at second slip.
Stand-in South African captain Dean Elgar was dismissed twice on the first day of his final Test match.
Elgar was out for four and 12 in an ignominious end to a Test batting career which yielded 5347 runs in 86 matches at an average of 37.92.
Elgar was bowled by Siraj in the first innings and caught by Virat Kohli at first slip off Mukesh Kumar in the second innings.
As he reluctantly left the field after his second dismissal Indian players ran to shake his hand.
Elgar's opening partner Aiden Markram made just two in the first innings but was more in command in the second innings and was unbeaten on 36 at the close.
However, Tony de Zorzi and debutant Tristan Stubbs both fell for one run.
South Africa won the first Test in Centurion by an innings and 32 runs in a match which lasted only three days.
The current match seems destined to be shorter.
