South Africa won the toss and chose to bat. Ashwell Prince was 23 not out at tea with Jacques Rudolph on 12. Australia are 2-0 up in the series.
Brett Lee and Clark, who two for 38 from 16 overs, shared the new ball and they found their line and length immediately.
South Africa struggled to get going, and their first run was scored in the fifth over when AB de Villiers drove a ball from Lee for a single.
The first boundary followed in the 10th over when Herschelle Gibbs, opening in place of injured captain Graeme Smith, drove Clark handsomely through the covers.
South Africa's troubles started four overs later when De Villiers lifted a drive off Clark and was neatly caught low down by Damien Martyn at cover for 12.
Three overs later the home side were reduced to 38 for two when Gibbs left a delivery from fast bowler Michael Kasprowicz and was bowled for 16.
Jacques Kallis and Boeta Dippenaar batted solidly for the rest of the morning session to nurse South Africa to lunch on 67 for two.
They were separated in the 10th over after lunch when Dippenaar, who hit seven fours in his 32, drove expansively at a delivery from Clark and was caught behind by wicketkeeper Adam Gilchrist to end a partnership of 59.
Lee bowled Kallis for 37 with an inswinger that nipped through the gate, reducing South Africa 106 for four in the ninth over before tea.
Kallis was captaining South Africa in the absence of Smith, who withdrew from the match with a finger injury. Dippenaar replaced Smith in the team.
Justin Langer, who is playing his 100th test, led the Australian team on to the field.
REUTERS DH HT1940