Skipper Graeme Smith came out to bat with a broken hand but could not save the match for South Africa as Australia won the third and final Test in Sydney by 103 runs on Wednesday to prevent a series whitewash and retain the top spot in ICC Test rankings.
Chasing an improbable 376 for victory, the South Africans, who were 62 for one overnight, folded up for 272 just 10 balls before the scheduled close of play on the final day.
However Proteas clinched the winner's trophy after triumphs in the first two matches in Perth and Melbourne.
Smith won the man of the series award for his aggregate of 326 runs and "exceptional leadership" in the series.
After Australia captain Ricky Ponting set up an exciting finale with his bold declaration on the fourth day, it was left to the South Africans to make a match of it but they collapsed to 171 for five by the 71st over leaving them with no choice but to fight for a draw.
Hashim Amla (59) and AB de Villiers (56) were the top-scorers for the Proteas but it was Smith who stole the show by coming out to bat after the fall of the ninth wicket.
Even with a broken right-hand finger, which has forced him to give the upcoming one-day series a miss, Smith decided to take the field after Dale Steyn's (28) dismissal in the 108th over.
The left-hander entered the ground to a rousing reception, with the SCG standing up to applaud the visiting skipper for his gritty decision.
Smith batted in discomfort for his three runs but managed to hold on for nearly seven overs with Makhaya Ntini (23 not out) at the other end.