Centre Jesse Kriel and hooker Malcolm Marx crossed for the Springboks, who dominated the breakdown and set piece but were unable to convert late pressure into a score that would have given them a sixth successive win.
Livewire centre Kurtley Beale and hooker Tatafu Polota-Nau scored tries for the Wallabies, who showed plenty of attacking endeavour but remain winless in the competition after back-to-back losses to the All Blacks.