India were 73 for two at lunch on Friday, an overall lead of 114.
Starting their second innings with a lead of 41 runs, the tourists lost both opening batsmen in the first 14 balls of the day and then were told Tendulkar could not bat in his usual position at number four because he had been off the field too long at the end of South Africa's first innings Thursday.
There was a six-minute delay before Ganguly appeared on the field and he was almost out first ball when he edged Makhaya Ntini between third slip and gully.
But captain Dravid and former skipper Ganguly batted solidly, adding an unbeaten 67 to prevent any further breakthroughs and taking India another step closer to ensuring at least a share of a series which is deadlocked at 1-1.
India restored the hard-hitting Virender Sehwag to his opening batsman role in a sign that the tourists intended to bat positively in an effort to win the match and series. But Sehwag slashed wildly at Dale Steyn in the second over to be caught behind for four.
Three balls later first innings century-maker Wasim Jaffer tried to avoid a bouncer from Ntini and the ball looped off his glove to AB de Villiers at first slip
Tendulkar was padded up but was told by match officials that he could not bat until another six minutes had elapsed because he had been off the field for the last 18 minutes of play Thursday.
The South African fielders asked whether Ganguly, who had to get ready instead, should be timed out but it was ruled that special circumstances applied because fourth official Murray Brown had only arrived in the Indian dressing room to inform them of Tendulkar's situation one ball before Jaffer was second man out.