Dean Elgar and Hashim Amla got South Africa through to tea on 153-2 at St George’s Park in Port Elizabeth, but crucially, Australia had put the brakes on the scoring.
The Proteas scored just 43 runs in the second session, with their run rate dropping to 2.31, and trail Australia by 90 runs.
Both Amla and Elgar reached their half-centuries after lunch, but Steve Smith will be the happier of the two captains as his seamers slowed down the home team.
With one session left to play, and with the new ball still to come, Australia will be looking to make the breakthrough before the end of the day.
Josh Hazlewood, who has got Amla out six times in the last seven games, nearly sent the South Africa batsman back to the dressing room, which was the most exciting bit of action after lunch.
Having done well in the first session, Elgar and Amla looked to pile on more runs after lunch, but they struggled against the fired up Australian attack.
Amla survived another good lbw shout by Hazlewood thanks to a big inside edge on to the pads.
The partnership was growing and the deficit was shrinking as Elgar and Amla continued to bat on.
The Proteas were 133-2, with Elgar on 46 and Amla on 45 at the halfway point in the second session, trailing Australia by 110 runs with eight wickets still in hand.
The run rate for the home side dropped during the second session as Hazlewood and Mitchell Starc started to get a lot of movement on the pitch.
Amla scored a single off Starc to bring up his 39th half-century. Elgar brought his own up when he edged Mitchell Marsh through the slips for four.
Australia 243 (1st innings): David Warner 63, Cameron Bancroft 38, Kagiso Rabada 5-96, Lungi Ngidi 3-51
South Africa 153-2 (1st innings): Dean Elgar 57*, Hashim Amla 54*, Pat Cummins 2-27
Photo: Deryck Foster/BackpagePix