David Warner hit two boundaries off Dale Steyn in the first over of the match but made only 12 before he was bowled by Steyn, edging an attempted cut into his stumps.
Chris Rogers made four before he was caught at short leg off Morne Morkel.
The tall fast bowler's first delivery of the match, after he replaced Steyn, was a bouncer which struck Rogers on the shoulder.
The next ball was another lifter which Rogers fended to the leg side, with JP Duminy diving to his right to take a good catch.
New cap Alex Doolan and Shaun Marsh added 48 for the third wicket before Doolan was caught at midwicket off Ryan McLaren for 27.
Marsh, who survived a sharp chance to Hashim Amla at gully off Morkel when he had 12, was 23 not out at lunch, while captain Michael Clarke was unbeaten on 11.
South African captain Graeme Smith said at the toss that he wanted to put Australia under pressure at the start of the series.
The pitch was well-grassed and Centurion has a reputation for helping fast bowlers on the first day.
Doolan and Marsh were Australia's only two changes from the team that was unchanged through a 5-0 Ashes series win against England, while South Africa opted for all-rounder McLaren to replace the retired Jacques Kallis.