Opening bowler Kyle Abbott bowled both Australian opening batsmen inside the first three overs and finished with four for 40, while unorthodox left-arm wrist spinner Tabraiz Shamsi took three for 36.
Mitchell Marsh and Matthew Wade made half-centuries but the next best batsman was tailender Chris Tremain, who made 23 not out.
South Africa, having clinched the five-match series by winning the first three games, picked what was effectively a back-up bowling attack, with fast bowlers Dale Steyn and Kagiso Rabada both rested along with leading spin bowler Imran Tahir.
They were replaced by Abbott and spinners Shamsi and Aaron Phangiso.
Abbott, who bowled a full length on a pitch which offered some sideways movement, bowled Aaron Finch with the third ball of the match and then bowled David Warner with the first ball of his second over.
George Bailey was leg before wicket to Dwaine Pretorius as Australia slumped to 12 for three.
It became 49 for five when Shamsi deceived Australian captain Steve Smith and Travis Head, trapping them both leg before, in the space of three balls.
Marsh and Wade put on 62 for the sixth wicket, while Wade and Tremain added 46 for the ninth wicket.
Marsh made 50 off 72 balls, while Wade hit 52 off 58 deliveries.