South Africa continued their excellent run of form to dominate a scrappy match in Port Elizabeth.
The Wallabies were shell-shocked after 23 seconds with Aphiwe Dyantyi collecting a wild Kurtley Beale throw to score.
The Springboks made it 12-0 on 20 minutes with Faf de Klerk profiting from some weak Wallabies defending.
Australia fought back with a gritty first-half performance - Reece Hodge drove through to make it 12-5 and Will Genia showed lightning pace to score from the Wallabies' best move of the game.
The difference was the impeccable kicking from Handre Pollard - his 2 penalty kicks and 2 conversions meant that the Springboks went into half-time 20-12 ahead.
South Africa controlled the rest of the game, with scoreboard pressure forcing the Wallabies into numerous mistakes and throwing away possession.
A final Pollard penalty provided the only points of the 2nd half - both teams visibly tiring in front of a partisan 46,000 crowd at the Nelson Mandela Bay Stadium.
The loss extends the Wallabies' poor form with only 2 wins in the last 10 matches.