South Africa were 64 for two at lunch after losing captain Graeme Smith and Hashim Amla inside the first six overs.
Ryan Harris made the first breakthrough when Smith played across the line and was leg before wicket for nine.
Mitchell Johnson followed up with his 50th Test wicket in seven matches since the start of the Ashes series against England when Amla was beaten for pace and trapped leg before with a full-pitched delivery.
Dean Elgar and Faf du Plessis steadied the innings with a solid unbeaten partnership of 53.
South Africa made three changes to the team which was beaten by 281 runs in the first Test at Centurion.
In a surprise move, left-handed batsman Quinton de Kock, who was not part of the original squad, was flown in and chosen to bat at number seven to fill the place vacated by injured all-rounder Ryan McLaren.
Elgar opened the batting in place of Alviro Petersen, who according to Smith was suffering from a stomach illness.
The left-handed Elgar saw both Smith and Amla dismissed before he scored his first run off the 20th ball he faced. His second scoring shot was a slog-sweep for six against off-spinner Nathan Lyon.
By lunch he had faced 78 deliveries and shown good composure against testing bowling.
In a third change, left-arm fast-medium bowler Wayne Parnell replaced left-arm spinner Robin Peterson.
There was almost a fourth change. The toss was slightly delayed while South Africa assessed the fitness of opening bowler Vernon Philander, who Smith said felt a twinge when he was warming up.
Australia were unchanged and almost immediately took over from where they had left off at Centurion, bowling straight and attacking the stumps in cool, overcast conditions on an easy-paced but well-grassed pitch.
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