Watch: Virat Kohli dives to his left to take stunning catch and send back Temba Bavuma
Kohli also became the sixth Indian fielder (who isn't a wicketkeeper) to reach the milestone.
The Proteas managed to score 210 courtesy a fine half-century by Petersen. The batter registered 72 runs off 166 balls with nine fours to his name.
But after Keegan's departure, the lower-order failed to add significant runs. In response to India's first innings score of 223, South Africa were bowled out for 210.
India, in their second innings, once again lost openers Mayank Agarwal and KL Rahul early. The visitors will be aiming to increase their lead and build some momentum. Kohli, in particular, will be hoping to carry on with his form after a half-century in the first innings.
Kohli registered 79 runs off 201 deliveries before losing his wicket to Kagiso Rabada on Day 1. He also hit 12 fours and a maximum.