India resumed at overnight 28 for three and lost Rohit Sharma for 11 before the break.
Dale Steyn, Morne Morkel, Kagiso Rabada and Vernon Philander picked up a wicket each.
Brief scores:
South Africa 1st innings: 286 all out
India 1st innings: 76/4 in 36 overs (Cheteshwar Pujara batting 26).