South Africa slipped to 225 for seven before Chris Morris and Kagiso Rabada took them to the close with an unbeaten partnership of 42.
Steven Finn picked up the crucial wickets of Dean Elgar, Hashim Amla and Faf du Plessis
Indian off-spinner Ravichandran Ashwin who picked up 5/32 in South Africa's first innings said he was not amused by the fact that focus of discussion during the Test series has been the nature of tracks.
Hashim Amla declared half an hour before the scheduled tea break but rain prevented the start of the West Indian reply after South Africa had amassed 552 for five on the second day of the first Test.