Australia declared on 565-5 halfway through Tuesday's first session to try and force a result.
Australia captain Michael Clarke, who made 259 not out, declared with a first innings lead of 115 over South Africa's 450, but his bowlers were unable to claim enough wickets to force a result in a test which lost a whole day to rain.
Jacques Rudolph (11) was adjudged lbw to spinner Nathan Lyon despite a television review to give Australia a late glimmer of hope but AB de Villiers (29) and Vernon Philander (one) ushered the tourists to the close of play.
"It was unfortunate not to get a result today," said Clarke, who was named man of the match for his record innings.
"But I think we fought hard with both bat and ball after the first day."
James Pattinson, the pick of Australia's bowlers, had given the hosts an early breakthrough by having opener Alviro Petersen caught behind by wicketkeeper Matthew Wade for five to leave South Africa on 6-1.
The 22-year-old seamer also bowled Hashim Amla for seven before lunch but the world's number one batsman was brought back to the crease for a no ball, the fourth wicket to be saved by the same infraction in the match.
The second wicket also came off Pattinson, who had a fiery exchange with Graeme Smith (23) before tempting the South African captain into an outside edge that Rob Quiney claimed well at gully.
Australia fruitlessly used both of their referrals as they ramped up the pressure on the South Africans and just when Amla and Jacques Kallis looked to be getting on top of the bowlers, they were separated.
Amla aimed a loose shot at a Peter Siddle delivery he could have left and the ball went straight to Mike Hussey at short cover.
Jacques Kallis, who backed up his first innings 147 with a 49, looked like he might guide South Africa to safety but fell to spinner Lyon with Clarke taking an excellent low catch in the slips.
By then, however, Australia's chance of a win was all but gone. Clarke, who resumed on 218 with his team on 487-4, again sparkled with the bat in the morning sunshine, adding 41 runs to his personal tally and taking the record for the highest individual score at the Gabba.
The 31-year-old shared a partnership of 228 with Hussey, who reached his 17th test century in a quickfire 128 balls with a rushed single before being dismissed on the next delivery he faced.
Morne Morkel claimed the wicket, his third, with substitute fielder Faf du Plessis taking a fine catch at full stretch at short cover.
Clarke was not going to be outshone, however, and he crashed a Dale Steyn delivery back over the bowler's head to bring up his 250 with his 28th four. His third double century of the year, which came from 398 deliveries in 582 minutes, eclipsed the 235 England's Alastair Cook scored at the Gabba in the opening test of the Ashes series two years ago.
It was a remarkable turnaround for Australia, who were reeling at 40-3 when Clarke took the crease on Sunday afternoon.
South Africa's number one test ranking is on the line in the series, which continues with matches in Adelaide and Perth after Brisbane. – Reuters