Clarke was at the crease with opener Ed Cowan, who lost his wicket nearing tea via a run out by Dale Steyn. He scored 136 (257b, 4X17).
Skipper Michael Clarke and Ed Cowan batted through the morning session to defy South Africa's bowlers and steer Australia out of trouble.
At lunch, Australia were 214 for three with opener Cowan nearing his first Test century on 98 and Clarke on 78.
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They had put on 174 runs for the fourth wicket after coming together late on Sunday with the home side tottering at 40-3 inside the 10th over.
Cowan moved past his highest Test score of 74 against India in Perth in January, seeking to consolidate his hold on an Australian opening berth.
Cowan had a couple of heart-flutters facing express bowler Dale Steyn but resolutely held his ground as the rock of the partnership with Clarke.
Early in the morning session Cowan tried to avoid playing Steyn only to get an inside edge which narrowly missed his stumps and went for four behind the wicketkeeper.
Clarke also had a scare when he fended off a Steyn lifter on 65 and the bowler narrowly failed to take a return catch on his follow-through.
Skipper Graeme Smith, without the services of incapacitated JP Duminy, brought himself into the attack with his off-spin to add variety to the five-prong pace attack.
Duminy, who can bowl spin, ruptured his Achilles tendon while warming down after Friday's first day's play and will be out for six months.