Rob Quiney took a diving, two-handed catch at gully to remove Kallis, who plundered 14 boundaries and a six; De Villers hit a hard cut shot to point, where Warner took a good catch.
Vernon Philander lofted offspinner Nathan Lyon for six to bring up 400 runs for South Africa in the 135th over but he was out soon after for 11, edging Siddle to Clarke at second slip.
Jacques Rudolph contributed 31 from 69 balls before he was caught by Quiney off Lyon's bowling to make it 426-7.
The South Africans went to tea at 434-7 and were all out 14 minutes after the break with Ben Hilfenhaus removing Dale Steyn (15) and Morne Morkel (0) to pick off the last two wickets. Rory Kleinveldt was unbeaten on 17, including two towering sixes. Hilfenhaus finished with 2-73 and Pattinson had the best figures of 3-93.
Steyn earlier had the benefit of a review after he was adjudged lbw to Hilfenhaus. The TV umpire overturned Rauf's decision, with replays showing the ball was going over the stumps.
The South Africans only had 10 available batsmen after J.P. Duminy ruptured his left Achilles in a training accident after the first day. He had surgery on Saturday and was expected to be sidelined for six months.
South Africa resumed Sunday at 255-2, after the entire second day was washed out by rain, with Amla on 90 and Kallis on 84. The pair rarely appeared to be troubled by the Australian attack.
Amla was hit on the front pad, just above the knee roll, by Siddle and asked Kallis if he should call for a review after Rauf had slowly raised his finger to signal out. He left the field without calling for a review, a decision he'll likely regret.
Amla stroked seven boundaries and a six in his six-and-a-half hour innings that spanned three days. He went to the crease with the Proteas at 29-1 after the dismissal of skipper Graeme Smith (10) on Friday and shared two important stands of 90 with Alviro Petersen (64) and Kallis.
Play resumed a half hour early Sunday in a bid to make up some overs and both teams stopped play at 11 a.m. and stood together in a line for a Remembrance Day ceremony.