Dropped from the Test side and nowhere near a mainstay of the 50-over format, either, Labuschagne (2-19) gained some much-needed confidence in the second ODI in Mackay on Friday.
After the Proteas appeared to be cruising to another big total at 3-179, Australia then tied down the middle-to-lower order and restrict the tourists to 277 as they were bowled out with five balls to spare.
Labuschagne was joined by recalled quick Xavier Bartlett and fellow seamer Nathan Ellis in taking two wickets each.
Adam Zampa ensured half of the wickets were taken by spinners when he took the final scalp, after previously dismissing Tristan Stubbs and Tony de Zorzi.
Matthew Breetzke (88) and Stubbs (74) threatened to take the innings away from Australia in their 89-run stand, before the former skied an Ellis delivery to Alex Carey without the gloves in the deep.
Ellis also claimed the crucial wicket of young gun Dewald Brevis, who lit up the recent T20 series.
Veteran Proteas spinner Keshav Maharaj took career-best figures in a thumping 98-run win in Cairns on Tuesday and will again loom large under lights.
Senuran Muthusamy will team up with Maharaj after debutant Prenelan Subrayen was reported for a suspect bowling action.
Captain Bavuma has been rested, replaced by Tony de Zorzi, as South Africa manage his workload after badly hurting his hamstring in the World Test Championship (WTC) final in June.
Tuesday night's match was Bavuma's first in any format since lifting the WTC mace by defeating Australia at Lord's.
Australia made just one change to the team, bringing in Bartlett for Ben Dwarshuis.
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