Australia were 156-4 in their second innings at close of play, still trailing by 170 runs after making a better fight of it than they had when crumbling under the South African attack earlier in the day.
But they were still on the rack despite Travis Head edging close to a century, unbeaten on 87 and to resume the final day along with nightwatchman Scott Boland on two.
It was a day of tumbling wickets as Australia, resuming on 3-1, were skittled out for 99 an hour after lunch, leaving them with a 326-run deficit after South Africa had scored 425–9 declared in the first innings.
Lanky fast bowler Marco Jansen took 5-33 in 11 overs as he ripped through the tourists, who posted their fourth-lowest total against South Africa.
Wiaan Mulder (2-14), Kagiso Rabada (2-33) and Anrich Nortje (1-5) took the other wickets, but Nortje only bowled 3.3 overs before a groin injury forced him from the field and out of the day’s play, leaving South Africa one bowler short as they put Australia in to bat again.
Sharp catching from South Africa contributed to Australia’s first innings collapse, with Simon Harmer taking three in the innings – the best a diving one-handed effort in the slips to dismiss Labuschagne.
It should have been a celebratory day for veteran Steve Smith, who reached the milestone of 11,000 Test runs as he top-scored with 28 in the first innings, but he struggled with a neck injury and did not come out to bat in the second innings, dropping down the order as he continued his treatment.
Australia’s second innings began in almost the same manner as the first had, with Nic Maddinson out early, edging Rabada to wicketkeeper Ryan Rickelton for eight runs.
But a 92-run partnership for the second wicket between Head and Labuschagne took Australia past their first innings’ total as South Africa’s attack began to tire.
However, an injudicious attempt to hammer spinner Harmer over the top saw Labuschagne caught near the boundary for 39 and he was followed by Matt Renshaw, hero of Australia’s 214-run victory in last week’s opening Test in Durban, who was bowled by Rabada for 11.
Beau Webster (8) was the 13th Australian wicket of the day as Harmer trapped him lbw, exposing the tail on the final day.
The first two days of the test were largely washed out, but South Africa staged a major fightback on Tuesday after being 110-6 with captain Temba Bavuma turning the match on its head with a majestic 173-run knock.