A maiden five-wicket haul for paceman Peter Siddle saw Australia finish day three of the third Test on top despite the best efforts of Mark Boucher.
Siddle, who finished with impressive figures of 5-59, took just 22 deliveries to capture the final four wickets and restrict South Africa to 327 at the SCG.
Boucher arrived at the crease with the Proteas in trouble at 166 for four, but put his head down to grind out a patient 89, spanning 265 minutes, before Siddle sent his stumps sprawling to secure his first Test five-for.
Boucher shared a 115-run partnership with Morne Morkel (40) to frustrate the home side before Siddle changed the course of the match with his inspired spell.
Having captured Morkel, Siddle then removed Paul Harris and Dale Steyn in quick succession before accounting for Boucher.
Australia openers Matthew Hayden and Simon Katich survived a nervous six-over period before stumps to progress to 33 without loss - a lead of 151.
Mitchell Johnson struck with the ball and in the field to leave South Africa in trouble before lunch.
Johnson removed Jacques Kallis for 37 - caught at first slip by Matthew Hayden - then ran out AB de Villiers with a brilliant piece of fielding.
Amla passed the half-century mark but was then involved in an unnecessary run out with de Villiers.
Pushing a quick single to Johnson at mid-on, Amla called for a single but watched in horror as de Villiers moved slowly out of his crease and was beaten by a direct hit at the wicketkeeper's end.
Debutant Andrew McDonald, who had done an excellent job strangling the South Africa top order, then trapped Amla with one that nipped back to leave the Proteas 166 for four before Boucher and Morkel combined to mount a fightback.
JP Duminy was the only batsman out in the afternoon session, given out lbw after playing back and caught on the crease by Johnson.
While Morkel rode his luck, playing and missing at a number of deliveries, Boucher also enjoyed some good fortune.
On 27 he played a ball from Nathan Hauritz on to his stumps only for the bails to stay rigid in their grooves.
Debutant left-arm paceman Doug Bollinger bowled without luck in search of his first Test wicket, having strong lbw appeals against Duminy and Morkel turned down by umpire Billy Bowden.
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