The home side have a fitness worry as seamer Morne Morkel, playing in his final Test before retirement from worldwide cricket, was forced from the field with a left side strain, but he did return to the pitch after the interval.
A persistent Australian attack that never went away ensured, however, that the home batsmen had to graft, and both Markram and De Villiers had to dig deep after tea to ensure that the hard work done in the first two sessions was not undone.
Perhaps the only person who wasn't thrilled to see the towering fast bowler take those giant strides out to the middle was the non-striker Bavuma, who was five runs short of three figures.
A South African team spokesman said the injury was in the same area that he damaged in a Test against Bangladesh in October, keeping him out of action for two months.
South Africa 2nd innings A. Markram c P. Handscomb b P. Cummins 37 D. Elgar (not out) 39 H. Amla c M. Marsh b N. Lyon 16 AB de Villiers c T. Paine b P. Cummins 6 F. du Plessis (not out) 34 Extras (lb-2) 2 Total (3 wkts, 56 overs) 134 Fall of wickets: 1-54, 2-79, 3-94.
The tourists, reeling from their ball-tampering scandal and led by new captain Tim Paine, had to endure chants of "where is Warner?" and "where is your captain?" from sections of the 17,023 home support at the Wanderers as a reminder of the bans handed to captain Steve Smith, his deputy David Warner and Cameron Bancroft.
Temba Bavuma was frustratingly left stranded on 95 in the final Test against Australia at the Wanderers but not before the diminutive right-hander put South Africa on top in their bid to seal the series.
Finishing with 5-83, Cummins now has 12 wickets in three innings at Johannesburg.
Renshaw was caught behind, quickly followed by Handscomb, who was bowled off an inside edge as he tried to withdraw his bat from a lifting delivery.
Wind Advisory issued ahead of severe storms
These storms are out ahead of the cold front, additional showers and storms are forming along the front as well. The greatest threat will be damaging winds and hail, although an isolated tornado can not be ruled out either.
Australia had been given a late jolt when Quinton de Kock caught Usman Khawaja brilliantly down the leg side off the bowling of Philander.
The opener ultimately fell to Kagiso Rabada for four runs as he finally knicked one to the slips.
The Proteas gloveman missed an easier take shortly after before replays showed he had seemingly been stung by a bee the moment the ball was set to land safely in his mitts.
But depending on what you believe, miracles have happened around this time of year before.
South Africa batted again and Aiden Markram, Dean Elgar and Faf du Plessis got starts as South Africa reached 134/3 at the end of the third day's play.
Captain Tim Paine (5*) and Pat Cummins (7*) will resume for the visitors on Sunday. "It was a good gesture from the Australians".
The usually pugnacious batsman, 31, repeatedly struggled to talk and tears ran down his face as he apologised to fans, team-mates, his family and the Australian public.
Second Test South Africa won by six wickets.