Allrounder Jacques Kallis bowled South Africa back into the first Test before Australia retaliated by taking three second innings wickets before the close of the second day on Friday.
Australia were dismissed for 308 in reply to South Africa's first innings of 205.
The home side had reached 70 for three, a deficit of 33 runs, at stumps.
Fast bowler Kallis took three for 51 to lead the fightback although the South Africans did themselves no favours by squandering four good chances.
Matthew Hayden and Ricky Ponting shared a partnership of 154 for the second wicket.
Ponting was dismissed for 74 with the last ball before lunch while Hayden went for 94 after lunch.