And Pattinson did his best to give Australia hope.
He coaxed a reckless drive from Petersen to have him caught behind and South Africa reeling at 1-6 before giving Amla a fright.
South African captain Graeme Smith also had an anxious moment on 12 when his leading edge off Peter Siddle failed to carry to the slips.
He was 17 not out at lunch with Amla unbeaten on seven.
Clarke overtook Cook's Gabba record when he thrashed Morne Morkel (3-127) down the ground for a boundary - one of 28 fours in his stunning 10-hour knock.
Next ball, Clarke was struck on the chest by Morkel but nothing could stop the prolific Australian captain.
He enjoyed a 228-run fifth-wicket stand with Mike Hussey (100) after they resumed on Tuesday at 4-487.
Clarke is Test cricket's leading run scorer for 2012, notching 1041 runs at 115.66.
He has averaged more than 60 with the bat since taking over the captaincy last August.
Hussey was also among the runs despite a deceptive record against the Proteas.
Against Dale Steyn, Morne Morkel and Vernon Philander, he had scored just 106 runs at a paltry 9.64 ahead of the Gabba Test.
But his rollicking knock made a mockery of the statistics.
The 37-year-old's 17th Test ton was his fastest - off 128 balls - but ended next delivery in a whirlwind finale.
Hussey survived a confident lbw shout by Vernon Philander on 99 after a review revealed an inside edge.
Next ball, Hussey almost ran out Clarke when he called for a quick single to bring up his ton.
Hussey was caught in the covers off Morkel (3-127) the next delivery he faced, ending an explosive 129-ball knock that included 13 fours.
In reply to the Proteas' 450 first innings dig, Australia recovered from 3-40 late on Sunday to launch a stunning counter-attack, also aided by opener Ed Cowan's 136 - his maiden Test ton.
- AAP