Zaheer Khan struck twice to leave the hosts reeling on 67-3 at lunch, Herschelle Gibbs with slice of luck is at the crease on an unbeaten 26.
The day began badly for the hosts when Jacques Kallis and express bowler Dale Steyn was ruled out due to injuries.
Skipper Graeme Smith fell to an ugly pull at Zaheer, Sachin Tendulkar taking a brilliant catch in the third over and South Africa were 28-3 at one point.
In sunny conditions, Smith attempted to give the innings some early impetus but chose the wrong delivery to pull and top-edged high over slip cordon, Tendulkar running back from first slip took a stunning catch at short fine-leg.
Hashim Amla, who made nought in the first Test, lasted nine balls for a single before playing across the line at Zaheer and making no contact.
Shanthakumaran Sreesanth was rewarded for some impressive swing and seam movement when induced AB de Villiers to nick a away going delivery only to gave a regulation catch to Tendulkar stationed at first slip.
South Africa 67 for 3 (Gibbs 26 n o Prince 17 n o; Zaheer 2 for 5, Sreesanth 1 for 28) Vs India