There was double delight as Kagiso Rabada speared one at disconcerting height and line at Ajinkya Rahane in the next over.
The veteran fended at it and the ball took off above wicket keeper Kyle Verreynne who stuck out a glove. It was enough to break the ball's momentum and it looped behind the keeper where captain Dean Elgar completed the catch.
With Kohli glaring down the wicket Rahane stood his ground, but was given out after a review.
It gave rise to optimism that SA could restrict India to a manageable total that would allow the hosts to complete a successful fourth innings chase.
However, in Virat Kohli India have a captain who is unlikely to depart the scene without forcing his will on proceedings.
Kohli, who constructed a patient 79 off 201 deliveries in the first innings, was even more obdurate on Thursday morning. His 28 not out came off 126 balls.
He found a willing ally in Rishabh Pant, who was more committed to advancing the scoreboard. Pant reached his 50 off 58 balls just before lunch.
It may prove to be a significant contribution in the context of the series, not just in weight, but timing. Every run Pant added to the India total lengthened the odds on SA performing another miracle act in the fourth innings.