It gave South Africa a lead of 177, which they stretched to 235 as they reached 58 for two at tea.
But South Africa will be without left-arm fast-medium bowler Wayne Parnell when they attempt to bowl out Australia a second time.
Parnell, who on Friday took two wickets with his first three deliveries of the match, pulled up with a groin injury after bowling three balls in his ninth over.
Team manager Mohammed Moosajee said Parnell had a strain, not a tear, but would nevertheless be unable to bowl in the second innings.
It left South Africa with only three specialist bowlers after bringing in a batsman for an all-rounder after losing the first Test in Centurion by 281 runs.
Australia struck back at the start of South Africa's second innings by dismissing both opening batsmen cheaply.
Captain Graeme Smith failed for the fourth successive innings when he was bowled off an inside edge by Mitchell Johnson -- the eighth time he has been out to the left-arm fast bowler in Tests.
The opening partnership of 20 with Dean Elgar was the highest by either side in seven innings of a series which features two strong fast bowling attacks.
Elgar was caught behind off Peter Siddle for 16. Parnell was not greatly missed in the first innings as Australia were already six wickets down when he was injured and the innings only lasted 57 overs. Vernon Philander took three for 68 and a hostile Morne Morkel claimed three for 63.
Resuming on 112 for four, Australia quickly lost David Warner, who added five to his overnight 65, and nightwatchman Nathan Lyon.
Steve Smith and Brad Haddin both survived chances as they added 40 for the seventh wicket before Haddin was bowled by Dale Steyn.
Johnson hit a quick 27 before he was bowled in the last over before lunch by off-spinner JP Duminy. In the previous over Johnson had been struck a heavy blow on the batting helmet by a bouncer from Morkel.
Smith made 49 before he was given out caught behind off a faint edge from Morkel after a review by South Africa.
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