Set an unlikely 430 to win, Australia were bowled out for a paltry 107, with fast bowler Morne Morkel taking five for 23.
It was a fittingly dismal end to the match for Australia after they were caught up in a ball-tampering scandal on Saturday which sent shockwaves through the sport.
Skipper Steve Smith was subsequently banned for one match by the ICC, just hours after he and vice-captain David Warner had stood down from their positions for the remainder of the match.
"It's been a horrible 24 hours -- I want apologise to our fans and those back home," said stand-in skipper Tim Paine.
The Australians had already woken to bruising criticism from their own chief executive and prime minister, as well as condemnation from around the cricket world.
It followed the admission by Smith and young batsman Cameron Bancroft that they had deliberately tried to change the condition of the ball on Saturday.
The day seldom got any better.
Tim Paine and his bowlers could not stop South Africa from taking their second innings total to 373.
Embattled opening batsmen Bancroft and Warner weathered a challenging 70 minutes before tea at the start of their second innings before the run-out of Bancroft sparked a collapse in which all ten wickets fell for just 50 runs in 19.3 overs and 99 minutes.
Bancroft fell to a direct hit from midwicket by South African captain Faf du Plessis after being called for a risky single by Warner.
Three overs later Warner edged Kagiso Rabada to AB de Villiers at third slip.
Both Bancroft and Warner were booed as they left the wicket but the near-capacity crowd's jeers grew in volume when Smith walked out -– and there were more boos after he was caught at gully off Morkel for seven.
It was Smith's last appearance in the series after being banned for one match for his role in the scandal, which means he will miss the fourth and final Test in Johannesburg, starting on Friday.
During Smith's short stay at the wicket, two wickets fell off successive balls from left-arm spinner Keshav Maharaj, with Usman Khawaja caught at slip off a ball that went straight on and Shaun Marsh prodding one which turned and bounced out of the rough to short leg.
The collapse continued when Mitchell Marsh and Pat Cummins fell to successive short-pitched balls from Morkel.
Mitchell Starc was hit on the helmet by another bouncer from Morkel. Two balls after a lengthy delay he gloved another lifter to short leg.
Nathan Lyon was run out without facing a ball as Paine tried to keep the strike and Josh Hazlewood was caught at third man to end one of the most humiliating episodes in Australia’s cricket history.
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First Published: March 26, 2018, 7:50 AM IST