Prop Coenie Oosthuizen put the visitors in front after six minutes and their advantage was extended with late tries from captain Jean de Villiers, Zane Kirchner and Willie Le Roux.
The win in front of 43,715 spectators at Lang Park was the Springboks’ first victory at the venue in eight attempts.
“I thought our defence was awesome,” Springbok coach Heyneke Meyer told a news conference.
“I truly believe we won the game firstly in our minds and secondly without the ball because the whole message was we needed to make more than 150 tackles.
“If they get momentum they are a very good side. I was very happy the way we attacked at the end.
“We really believed we could win. We wanted to show if you work together nothing is impossible.”
The win puts South Africa on top of the Rugby Championship with three wins ahead of a meeting with New Zealand, who are also unbeaten, and Meyer cautioned his side to stay grounded ahead of next Saturday’s clash at Eden Park.
“A lot of things worked, but we need to keep our feet on the ground and stay humble because next week is a bigger challenge,” he said.
The talk leading into the game surrounded Australia’s exciting back line but it was the Springboks who ran amok, especially in the last quarter.
Conversely, Australia failed to score a try against South Africa for the first time since 2001 as the Springboks bettered their previous record win in Australia, a 12-point victory in 1971.
Oosthuizen gave South Africa the perfect start in the sixth minute. After Nick Cummins failed to keep Morne Steyn’s long kick in play, South Africa won their lineout and Oosthuizen, on the field as a blood-bin replacement, brushed aside Scott Fardy and Quade Cooper to score.
Cummins looked like he could make amends for his earlier error when a line-break sent him bearing down on the South African try-line, but he slipped over just inside the 22 with one man to beat.
Three penalty kicks from Steyn and two from Christian Leali’ifano followed as the Springboks extended their lead to 16-6 at halftime, although it could have been worse for the Wallabies had Quade Cooper not produced a fine tackle to stop le Roux in the right corner three minutes before the interval.
On the hour mark, wing Bryan Habana’s fine run and chip forward into the 22 led to an easy chance for de Villiers to run in a try.
Four minutes later, a superb pass inside on the right wing from le Roux set free Kirchner to extend the lead six minutes later.
Then loose play from Quade Cooper gifted the Springboks a turnover in midfield and Duane Vermeulen fed le Roux who raced over for a try of his own 10 minutes from time.
Such handling errors were the chief cause of frustration for Wallabies coach Ewen McKenzie who is still searching for his first win after three games.
“It doesn’t matter who you play if you drop the ball in key moments and they counter-attack it’s hard work,” McKenzie said.
“You’ve got to create opportunities and you’ve got to grab them. We didn’t quite get there. That was the frustrating thing. We got up there in front of the goalposts four times and turned the ball over.
“There are bits of the game that are improving slowly but you are judged on the scoreboard and that’s not an acceptable outcome. We made it too easy for them in the second half.”
In a match that threatened to boil over on several occasions each side had a man sin-binned, Willem Alberts for a deliberate knock-on in the first half and Michael Hooper after a dangerous tackle on Habana after the interval.
(Editing by John Mehaffey)