Spinner Simon Harmer took four wickets to lead South Africa's fightback as they bowled out India for 189 after the hosts managed a slender lead of 30 on day two of the opening Test on Saturday.
India lost regular wickets to survive just 62.2 overs in response to South Africa's first innings total of 159 on a tricky pitch to bat at Kolkata's Eden Gardens.
South Africa were 18-1 after Ryan Rickelton was trapped lbw off Kuldeep Yadav for 11 at the stroke of tea. Aiden Markram was batting on three.
Bowlers have ruled the low-scoring contest with Indian opener KL Rahul's 39 being the top score between the two teams.
India skipper Shubman Gill went out retired hurt for four with a neck spasm and did not return to bat in the innings that ended in the second session.
India went into lunch at 138-4 and Dhruv Jurel started with two fours after the break before Harmer got the batter caught and bowled for 14 to trigger a collapse.
Ravindra Jadeja took India into the lead with a boundary but fell lbw for 27 off Harmer and India sunk further when pace bowler Marco Jansen had Kuldeep Yadav caught behind for one.
Harmer had Axar Patel out for 16 to return figures of 4-30. Jansen claimed three wickets.
The hosts resumed on 37-1 with overnight batters Rahul and Washington Sundar, who made 29, extending their partnership to 57 in a grinding first hour.
Returning Rishabh Pant hit a 24-ball 27 on a pitch with inconsistent bounce and more turn expected.
Sundar hit two fours and one six in his otherwise laboured knock before falling caught behind to Harmer.
Gill walked out to loud cheers but his stay was limited to three balls as he swept Harmer for a four at backward square-leg and then held his neck in pain.
The physio soon arrived and Gill walked back to the pavilion.
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Rahul kept up his hard work from day one when he made 13 off 59 balls and on day two looked more assured until his departure off Keshav Maharaj.