India were 160 for eight at tea on Saturday with South African fast bowler Makhaya Ntini taking five for 38.
Mahendra Singh Dhoni made 47 for India before he was caught behind in the last over before tea after adding 59 for the eighth wicket with Zaheer Khan.
After only 4.3 overs of play were possible before lunch, the sun came out in the afternoon to give South Africa the opportunity to hit back after losing the first Test in Johannesburg by 123 runs. The third and final Test starts in Cape Town Tuesday.
India limped to 47 for four at lunch after Ntini dismissed both overnight batsmen, Sachin Tendulkar and Wasim Jaffer.
India, resuming on 38 for two, lost Tendulkar to the fifth delivery of the day. Ntini produced a virtually unplayable ball to Tendulkar that cut back sharply and kept low to trap India's star batsman leg before for nought.
Jaffer followed nine balls later when he played an injudicious pull shot that looped gently to Andre Nel at mid-on. He made 28.
VVS Laxman and Sourav Ganguly kept the South Africans at bay after lunch, putting on 38 for the fifth wicket. Ganguly made 26 but it was an unconvincing innings.
Three of his four boundaries were scored off edges before he was out tamely, steering a lifting ball from Ntini to Herschelle Gibbs at gully.
Laxman looked more solid but appeared to misjudge the length of a ball from Andre Nel. Going back deep in his crease he seemed to expect the ball to lift but it shot through at bail height to bowl him.
At that stage India were 85 for six. Dhoni was struck on the right hand by the first ball he received from Ntini. He had suffered bad bruising on the middle finger of the same hand while keeping wicket and told journalists Friday he was not sure he would be able to play in the third and final Test.
He received treatment and looked in pain but continued batting without showing further signs of discomfort.
Dhoni and Anil Kumble resisted for 41 minutes. Andrew Hall, the fifth bowler to be used, made a breakthrough with his first ball when Kumble fended a lifting ball to Hashim Amla at short leg.
Dhoni then played some attacking strokes as he and Khan posted a half-century stand. But two balls before tea Dhoni edged an extravagant drive and wicketkeeper Mark Boucher flung himself to his right to hold a good catch.