India were in the box seat after bundling out South Africa for 159 at Eden Gardens where inconsistent bounce has been a bane for the shot-makers from both sides.
It was evident in India's reply too as they managed 189 to be left with a lead well short of their own expectations.
South Africa finished day two on 7-93 - only 63 runs ahead with three wickets in hand.
Skipper Temba Bavuma led their fightback with 29 not out and with Corbin Bosch on one at the other end.
India were one batter short in the first innings after skipper Shubman Gill retired hurt with a neck spasm, having made four.
Bowling coach Morne Morkel was non-committal about Gill's chances of batting in the second innings.
"I think we first need to determine how he got the neck stiffness, maybe it's just a bad night's sleep," he said, denying that it was the result of Gill's all-format workload.
"Shubman is a very fit guy. He looks after himself very well. So it was just unfortunate that he woke up with a stiff neck."
Off-spinner Simon Harmer (4-30) dragged South Africa back into the contest after India had resumed on their overnight score of 1-37.
Washington Sundar (29) hit Keshav Maharaj for a six but could not carry on and was caught at slip off Harmer's bowling.
Gill opened his account with a four but immediately walked off the field rubbing his neck.
Returning from a foot injury that kept him out of the home series against West Indies, Rishabh Pant (27) had the South Africa players on their toes right after he walked in.
Pant was surprised by a leaping Maharaj delivery, which he guided towards slip where Markram was too startled to react in time and take the catch.
Pant rubbed salt into Maharaj's wound by stepping out to the next ball and hitting it for a six over mid-off.
The spinner found some solace when he had Rahul (39) caught at slip but Pant scored freely.
Bosch brought relief to the South Africa camp when he dismissed Pant caught behind with a bouncer.
Jadeja contributed 27 but lack of partnerships hurt India, who folded half an hour before the tea break.
In doing so, the 36-year-old joined a select group of all-rounders to reach 4000 runs and take 300 wickets in tests, joining — India's Kapil Dev, England's Ian Botham and New Zealand's Daniel Vettori.
Jadeja returned to haunt South Africa with the ball after the Proteas came out to bat for the second time in the match.
After Kuldeep Yadav got rid of Ryan Rickelton for 11, South Africa's frontline batters surrendered to Jadeja's (4-29) relentless left-arm spin.
"We need to obviously try and get as many as we can and get past 100," Harmer told reporters.
"If we can get to 150, that would be incredible but it's obviously quite difficult."
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