Resuming on 30 for no loss, South Africa needed 42 overs to score the remaining 153 runs for a memorable win and the moment came soon after lunch when Hashim Amla flicked Michael Clarke behind square leg for two runs.
In a match where Smith struck two fifties, JP Duminy scored his maiden hundred and Ponting scored 101 and 99, Dale Steyn was adjudged Man of the Match for his match haul of 10 for 154 besides the crucial 76 he scored in the first innings.
Graeme Smith was the lone South African wicket to fall in the second innings. The South African captain was trapped leg before by Nathan Hauritz after making a 94-ball 75 with 10 boundaries in it.
Fellow opener Neil McKenzie (59) and Amla (30) remained not out after guiding the team to a historic win.