South Africa scored 23 unanswered points in the first half after an early Wallabies penalty, but couldn’t maintain that momentum.
Hooker Adriaan Strauss and full-back Zane Kirchner went over for tries inside 15 minutes against a creaking Wallabies defence and South Africa led 23-3 after 32 minutes.
But it took until the 72nd minute for wing Willie le Roux to cross for the third try and, despite scrambling desperately at the end, the home team didn’t find the fourth try that might have boosted their title chances.
New Zealand played in Argentina later last night.
The Boks and All Blacks meet at Johannesburg’s Ellis Park in a tournament decider on Saturday.
For most of the second half, a battling Australia, outplayed almost everywhere, held up the South Africans while never threatening to stop a losing run at the Cape Town ground that dates to 1992. The Wallabies then pounced for a late consolation score when a cross-kick found debutant Chris Feauai-Sautia free on the left flank to touch down in the 78th – over 70 minutes after the Australians’ first points.
South Africa’s players also didn’t celebrate the victory as eagerly as they might have despite successive wins over Australia to win the Nelson Mandela Plate.