The hosts will the happier of the teams as they trail by just seven runs and have Travis Head still at the crease and looking in sublime form on 78 off just 77 balls.
After being put in to bat by home captain Pat Cummins on a green looking surface at the Gabba, the Proteas were quickly staring down the barrel as they slipped to 27-4.
Skipper Dean Elgar (3) was the first batter to depart as Mitchell Starc strangled the opener down the leg side before Cummins nicked off Rassie van der Dussen (5).
Seamer Scott Boland continues his remarkable start to his Test career which sees him average less that 10 with the ball as he picked up two wickets in the same over.
The Victorian had Sarel Erwee (10) caught by Cameron Green in the gully and then trapped Khaya Zondo for a duck in the same over.
Temba Bavuma and Kyle Verreynne steadied the rocking ship somewhat and the tourists went to lunch on 84-4.
The South African pair cracked on after the interval with Verreynne particularly looking to be take the aggressive approach it seemed to pay dividends.
The wicketkeeper and Proteas Test vice-captain added a valuable 98 but Bavuma was bowled by Starc for 38 to leave the Proteas on 125-5.
Marco Jansen (2) and Keshav Maharaj (2) did not last long while at the other end Verreynne went past the milestone of fifty but his innings was cut short by spinner Nathan Lyon (3-14) on 64.
The Proteas needed a quick start with the ball and they could not have asked for a better one when Kagiso Radaba dismissed David Warner with the very first ball of the innings, brilliantly caught at short-leg by Zondo.
Jansen then had the in-form Marnus Labuschagne (11) caught in the slips while Anrich Nortje dismissed Usman Khawaja (11) cheaply as the hostss slipped to 27-3.
Head then came out ultra-positive and together with Steve Smith added 117 for the fourth wicket.
South Africa had a good end to the day though when Nortje castled Smith (36) and Rabada got rid of nightwatchman Boland with was the final ball of the day.