The Proteas’ 3-1 success is their first series victory on home soil over Australia since 1970.
South Africa's bowlers needed seven wickets on the final day of the fourth test in Johannesburg as Australia faced a record run chase.
And Vernon Philander delivered the blows, taking 6 for just 12 runs earlier to clinch a third straight victory for South Africa, as Australia were all out for 119 in pursuit of a fanciful 612 victory.
The Kangaroos defeat is the heaviest of any team in terms of runs and tests since 1934.
"We can't hide from the fact that purely on skill they outplayed us," new captain Tim Paine told reporters on Tuesday.
But the fall-out from Australia's ball-tampering scandal also had a major effect on the performance of the team, Paine added.
"I thought we were going to be better than we were. It obviously had more of an effect on guys than we probably knew ourselves."
Meanwhile the Australian cricketer's association has called for a reduction in the bans delivered last week: to Steve Smith, David Warner and Cameron Bancroft, for their part in a ball tampering scandal.
“The contrition shown by these men is extraordinary, absolutely extraordinary,” Australian Cricketers’ Association president Greg Dyer said.
Captain Steve Smith and vice captain David Warner, were handed 12 month suspensions, while Cameron Bancroft was banned for 9 months.
“The distressed faces have sent a message across the world as effective as any sanction could be."
Paine said Australia would now reflect on what had happened. "Now we have the opportunity to go home and start again almost," he concluded.