Kohli was ruled out on the morning of the match due to a back spasm, after India were bowled out for 202 by South Africa on the first day of the second Test in Kohli's absence.
Stand-in captain KL Rahul scored 50 runs in Kohli's absence.
Proteas left-arm pacer Marco Jensen claimed 4-31, while Kagiso Rabada and Duane Olivier both claimed 3-64.
Olivier dismissed Cheteshwar Pujara and Ajinkya Rahane in successive deliveries.
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