Usman Khawaja batted purposefully in the morning session as he headed towards a second innings century.
Kagiso Rabada gave South Africa's victory push an early kick by dismissing Mitchell Marsh LBW via a controversial DRS call.
The cracks on the WACA surface had widened significantly on the fifth morning when the umpires came to inspect.
Kagiso Rabada had Mitchell Starc LBW to complete his five-fer.
Jean-Paul Duminy trapped Usman Khawaja plumb in front three short of his century.
Peter Nevill and Josh Hazlewood frustrated the South African in the second session with a half-century stand as edges dropped short or flew away from the close-in fielders.
Peter Nevill scored a half-century as Australia delayed the inevitable in the second session.
Faf du Plessis kisses Kagiso Rabada on the forehead after he picks up his fifth wicket.
Faf du Plessis was lavish in his praise of Kagiso Rabada at the press conference.
South Africa registered a historic win to take a 1-0 lead in the three-match series.