The Proteas went to lunch on 395/7, having bowled India out for 334 in their first innings.
The two not out batsman are Faf du Plessis and Robin Peterson - both on five.
SCORECARD: South Africa v India
Earlier, Jacques Kallis made a century in his final Test for South Africa to say farewell with a 45th career hundred.
Kallis went to three figures with a nudge to mid-on and celebrated by removing his helmet and lifting both arms in the air as he faced the team dressing room.
India's fielders and coach Duncan Fletcher also applauded the 38-year-old all-rounder.
Kallis was dismissed for 115, but not before he moved ahead of India's Rahul Dravid into third spot in the all-time Test run-scorer list (by a single run).
Kallis is second on the all-time list of century-makers in Test cricket behind India's Sachin Tendulkar, who finished with 51. He announced on Christmas Day that he would retire from Tests after his 166th appearance for his country at Kingsmead - the same ground he made his debut at as a 20-year-old prodigy in 1995.