Stunning tries from prop Ben Alexander and wing Digby Loane plus a conversion and penalty from James O'Connor helped Australia to a 15-6 interval lead, with Morne Steyn kicking two penalties for the Springboks in Sydney.
Further tries followed from O'Connor, Stephen Moore and Adam Ashley-Cooper, with O'Connor adding all three conversions and a penalty for a personal haul of 19 points.
Chiliboy Ralepelle and John Smit crossed for the Springboks but those tries will have been little consolation for coach Peter de Villiers and his injury-hit side, who were second best in all facets of the game.
The Wallabies had come in for plenty of criticism following that shock reverse against the Samoans, but they looked a completely different proposition as they hit the Springboks with a rapid-fire try double inside the first 12 minutes.
Quade Cooper launched the attack for the first score from inside his own 22, stepping inside a host of tacklers to break clear. The fly-half found Kurtley Beale and O'Connor in support before the ball was worked to the left touchline for Rocky Elsom to allow Alexander to canter over.
O'Connor added the extras and straight from the restart the second try quickly followed. Scrum-half Will Genia made the break from deep on this occasion and fed Ioane, who beat a weak tackle from Gio Aplon to cross for an unconverted try.
Australia's impressive handling was proving too much for South Africa to handle, and only a spilled pass from Cooper prevented another try for Robbie Deans' side.
The visitors looked to respond with some good carrying by debutant number eight Ashley Johnson, but their attacks were ponderous compared to the imaginative play of their opponents and were easily repelled.
Steyn got the Boks on the board on the half hour mark with a penalty after Ashley-Cooper slowed down the ball illegally at a ruck, but O'Connor responded with a penalty of his own to restore Australia's 12-point advantage.
And the Wallabies came close to further extending that lead as Beale and O'Connor linked superbly on the counter-attack to send the full-back racing into the South Africa 22, but lock James Horwill could not hold his pass.
A powerful rolling maul did at least allow Steyn to knock over his second penalty on half-time and keep South Africa in the game, but the ponderous Boks had plenty of work to do.
But the game was killed off within eight minutes of the restart as Australia wrapped up a try bonus point.
Firstly, Cooper exploited a gaping hole between Juan de Jongh and Wynand Olivier to send out a low pass that O'Connor stooped to gather and score, the wing adding the extras.
Then Moore chose a brilliant angle to race onto a flat Cooper pass and beat Aplon to dot down by the posts, the score was confirmed by the video referee and converted by O'Connor to make it 29-6.
O'Connor added his second penalty shortly before more skilful offloading from Cooper created the fifth try as his flip pass sent Ashley-Cooper into space, with Steyn missing a tackle to let the centre flop over the line. O'Connor was once again on target with the extras.
The visitors briefly rallied with replacement hooker Ralepelle being bundled over from another effective maul, with substitute Patrick Lambie converting, before captain Smit burrowed over in the final minutes.
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