South Africa took four wickets, including David Warner first ball after he resumed on 200, but a half-century from Alex Carey strengthened Australia's grip on the second Test in Melbourne on Wednesday.
At lunch on day three, the hosts were 479-7 in their first innings, leading by 290, with Carey not out 62 and a ginger Cameron Green, batting with a fractured finger, on 14.
They began on 386-3 with Travis Head on 48 and Carey nine after a herculean unbeaten 200 from Warner in his 100th Test in gruelling heat on day two.
The veteran opener retired exhausted with severe cramp after making his third Test double century, but he resumed his innings when Head was out for 51, walking out to huge applause.
He told host broadcaster Fox before play began that he had a "rough night's sleep".
"I probably woke up six or seven times," he added, and was bowled first ball by an Anrich Nortje yorker as Australia lost three wickets for five runs.
Temperatures were much cooler than the 37 degrees Celsius (98.6 Fahrenheit) on Tuesday, with conditions overcast and humid -- generally favourable to the bowlers.
And the ever-dangerous Nortje took advantage, bowling Head in the third over before snaring a bewildered Warner next ball.
Pat Cummins fended off the hat-trick delivery, but he did not last long.
The Australian skipper fell to the third ball he faced when South Africa successfully reviewed a caught behind decision off Kagiso Rabada's bowling that was initially denied by the umpire.
Carey was joined by Nathan Lyon and they steaded the ship.
Lyon made an entertaining 25 before holing out to Khaya Zondo off Lungi Ngidi
Ahead of play, Green, who took 5-27 in South Africa's first innings, was ruled out of bowling again in Melbourne -- and the third Sydney Test -- with a fractured finger, but bravely came out to bat.
Carey was flawless and brought up a superb fourth Test half-century off just 66 balls with a third consecutive four off Ngidi.