Springboks coach Peter de Villiers packed his side with Test match know-how - the starting XV had 810 caps between them - but they suffered a third defeat from three Tri Nations matches, with a losing bonus point coming as scant consolation.
Three penalties from James O'Connor and a well-worked try from Pat McCabe, all in the second half, did the damage for the Wallabies, who joined New Zealand on nine points at the top of the table.
On the evidence of this, there is a lot of improvement still to be done if South Africa are to win a third world title in New Zealand this autumn.
The hosts edged ahead with a Francois Steyn penalty in the second minute after Australia skipper Rocky Elsom was penalised for a dangerous tackle on Bakkies Botha off the ball.
Steyn produced a try-saving tackle to deny Elsom and Butch James doubled the Boks' lead with a 16th-minute penalty in what started off as a high-octane encounter.
James missed a second penalty attempt four minutes later and South Africa centre Jacques Fourie was denied a try by the television match official, who judged he had knocked on as he battled with Quade Cooper to bring a high kick under control.
James failed with a drop-goal while James O'Connor and Steyn were also off-target with further penalty and drop-goal attempts respectively as the score remained 6-0 to South Africa at the interval.
Australia turned the match on its head early in the second period, halving their hosts' lead thanks to O'Connor's 44th-minute penalty.
And the Kings Park crowd were silenced completely when McCabe rounded off a slick passing move to score the first try of the match and move Australia 8-6 in front. O'Connor failed to add the extras.
James' penalty edged the Springboks back in front but an infringement by Tendai Mtawarira at a ruck allowed O'Connor to strike again after 65 minutes.
O'Connor stretched the lead to five points with a 74th-minute penalty and, despite desperate attempts by South Africa to find a match-levelling try, the Wallabies held on.
South Africa host New Zealand in Port Elizabeth next Saturday before the series concludes with Australia meeting the All Blacks in Brisbane on August 27.
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