The Springboks scored the only try of the match through their centre, Robbie Fleck, midway through the second half - avoiding a fifth successive defeat - and then kept Australia camped largely in their own half with some fierce tackling.
The 10-9 victory gave the All Blacks their third Tri-Nations title because the New Zealanders, on 12 points, can no longer be overtaken. Australia play the Kiwis in the final match of the competition, in Sydney in two weeks' time.
All Australia's points came from their full-back, Matt Burke, who kicked three out of four penalties, while their back division struggled.
The Wallabies' only real try-scoring chance came in the opening three minutes, but Ben Tune's pass to an overlapping team-mate was ruled forward.
A swirling wind dominated the first half, with the Springboks' stand- off, Jannie de Beer, landing one of two penalty attempts to put his side in the lead, before Burke levelled the scores two minutes before the interval. He added a second after an hour, but it only served to inspire the Springboks.
Four minutes later Fleck scored after the scrum-half Joost van der Westhuizen had been stopped just short of the line, the centre powering past Mark Connors to score.
De Beer converted but Burke narrowed the gap to a single point shortly afterwards.
South Africa: Try Fleck; Conversion De Beer; Penalty De Beer. Australia: Penalties Burke 3.
SOUTH AFRICA: P Montgomery; D Kayser, R Fleck, B Venter, P Rossouw; J de Beer, J van der Westhuizen (capt); R Erasmus (R Kruger, 65), A Venter (B Paulse, 40), A Vos, A van den Berg, S Boome (M Andrews, 60), C Visagie, N Drotske, O du Randt (O le Roux, 61).
AUSTRALIA: M Burke (J Little, 74-78); B Tune, D Herbert, N Grey, J Roff; T Horan, G Gregan; T Kefu (T Strauss, 40), D Wilson (capt), M Cockbain, T Bowman (M Connors, 60), D Giffin, A Blades, P Kearns, R Harry (P Noriega, 50).
Referee: C Hawke (New Zealand).
Gary Teichmann, the 32-year-old former South Africa captain, has confirmed he will join Newport next season.Reuse content