South Africa made 450 and then took three Australia wickets to take control of the first Test in Brisbane.
After the second day's play was washed out the tourists were keen to push on from their position of 255-2 at the end of day one.
Hashim Amla knocked off the 10 runs he needed to reach his century but was soon trapped lbw by Peter Siddle, ending a partnership of 165 with Jacques Kallis.
The veteran reached a hundred of his own - the 44th of his Test career - in the next over and found another good ally in AB de Villiers, the pair taking their stand to 73 at lunch.
However, just four overs into the afternoon session Kallis cut James Pattinson to gully having made 147 and de Villiers (40) fell shortly afterwards, Warner taking the catch at point off the same bowler.
The runs then dried up as the Aussies hit back, Vernon Philander edging Siddle to slip soon after hitting a six off Nathan Lyon before Jacques Rudolph gave Quinney a second catch off Lyon (2-136).
Dale Steyn (15) successfully appealed an lbw decision against him but Ben Hilfenhaus removed both he and Morne Morkel to close the innings after debutant Rory Kleinveldt had hit the unfortunate Lyon for back-to-back sixes.
Australia were quickly on the back foot when they took to the crease as the Proteas reduced them to 40-3.
David Warner was sent back in the fifth over with Steyn inducing an edge to Kallis at slip, before Morkel (2-25) removed both Quinney and Ricky Ponting in successive overs.
However, opener Ed Cowan (49 not out) and captain Michael Clarke (34 not out) steadied the ship with a confident 71-run partnership to give the hosts hope of saving the game, resuming as they will on 111-3.