They will begin the third day on Sunday trailing South Africa by 378 runs.
They created few other opportunities on a helpful wicket and with a relatively new ball, and with rain predicted later in the test, Australia's hopes hinged on restricting South Africa to a first inning score they could surpass quickly and build a first innings lead. As low points go, that is stratospheric. If it was helping Bavuma to a hundred or just because someone had a word in his ear that inspired him, it doesn't matter, because he showed here that he can should contribute a lot more with the bat than he has done hitherto in his Test career.
Renshaw, back after Cameron Bancroft was preferred for the Ashes last summer and then this tour, chased a wider one from Philander (3-17) and was caught behind. The Australian Skipper Tim Paine and his counterpart Faf Du Plessis had a long talk after the toss was concluded which is itself a new thing.
Australia's top order was nearly unrecognisable from the corresponding group in Cape Town.
Opening batsmen Joe Burns and Matt Renshaw were out for four and eight respectively while Peter Handscomb was out first ball for nought to leave Australia reeling at 38 for three.
Burns edged Kagiso Rabada to second slip for the first wicket down, with du Plessis taking a diving catch.
But he was more expansive after the drinks break as South Africa looked to drive home their growing advantage. He was then hit on the finger in the final overs while facing Morkel.
Earlier in the day, Nathan Lyon had an appeal that was unsuccessful against ab de Villiers; replays showing the ball was set to miss leg-stump. Handscomb simply shook his head in disbelief.
Debutant Sayers found movement - and earned comparisons to Vernon Philander due to his pace and bowling style - but couldn't find a first Test wicket. Khawaja, rounding out an all-Queensland top three, looked in good touch, but Marsh's strokeplay seemed about as fluent as his Xhosa.
There were no signs of nerves in the 90s for Bavuma when he reverse-swept Lyon for his 13th boundary, but he missed out on three figures when Cummins removed Morne Morkel - playing his last global - first ball.
South Africa, resuming at 6-313, built a formidable first-innings total of 488 as Temba Bavuma (95 not out) combined with the lower order before being stranded just short of a second Test century.
But De Villiers and Bavuma steadied the innings again with a fifth-wicket partnership of 52, before two late wickets lifted Australia at the Wanderers.
Meanwhile, Aiden Markram reached his century from 152 balls in what was been a batting masterclass.