Usman Khawaja and Peter Nevill showed admirable resistance on day five as the home side batted until late in the second session.
But it wasn’t enough to prevent Australia from losing the opening Test of a home summer for the first time since 1988 when a West Indies attack featuring Malcolm Marshall, Curtly Ambrose and Courtney Walsh humbled them in Brisbane.
On Monday, South Africa secured victory despite being a bowler down from the moment spearhead Dale Steyn suffered a series-ending shoulder injury early in Australia’s first innings.
Khawaja top-scored with 97.
Nevill, who was dropped on two, soaked up 153 deliveries and almost four hours in an unbeaten knock of 60.
But Nevill and the tail were left with far too much work to do as Australia were bowled out for 361, having resumed at 4-169 on Monday.
Proteas paceman Kagiso Rabada was inspirational in the absence of Steyn, swinging the ball both ways at pace to grab five wickets and be named man of the match.
The result follows Australia’s shambolic 3-0 series loss in Sri Lanka earlier this year.

Australia haven’t lost four Tests in a row since their calamitous tour of India in 2013. That debacle delivered a reminder of their subcontinent struggles, exposed bitter divides in the squad and essentially cost coach Mickey Arthur his job.