South Africa captain Graeme Smith has been left with his left hand in plaster after a century from Australia's Michael Clarke was negated by a Proteas fightback late on day two of the third Test at the SCG.

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In reply to the hosts' challenging first-innings total of 445, the tourists will enter day three on 125 for one with Hashim Amla (30) and Jacques Kallis (36) to resume on a pitch showing signs of wear and tear.

Smith was forced to retire hurt on 30 and go to hospital for x-rays after being struck by a rearing delivery from Australia paceman Mitchell Johnson late in the day.

He returned to the ground with his left hand and wrist in a plaster cast and will only bat again if the Proteas have a chance of winning or drawing the Test.

A decision has yet to be made as to who will take over the captaincy for the remainder of the game.

Neil McKenzie, who laboured for nearly two hours, was the only wicket to fall in the South African innings, trapped lbw by Peter Siddle.

Clarke's ton - his first Test century on the SCG - underpinned Australia's large first innings total before a crowd of 30, 293.

His 142-run partnership with Johnson (64) swung the game Australia's way.

Resuming on 77, Clarke showed his intent from the opening ball, cracking Makhaya Ntini through the covers for four.

He brought up his 10th Test century with a quick single before sprinting towards the members' stand with arms raised in triumph, seemingly oblivious that there was a third umpire's decision pending.

Clarke, who was dropped on 12 and 69, survived the close call and went to lunch with hopes of reaching 150.

But in his opening over, JP Duminy enticed a return catch from the Australia vice-captain, who left his home ground to a standing ovation.

Clarke's purposeful knock - a mix of exquisite drives, intelligent running and rigid defence - contained 17 fours in a 373-minute stint at the crease.

Johnson, who was put down by Kallis on 18, clubbed 11 boundaries en route to his best score at Test level before being snapped up at first slip by Smith off Dale Steyn, who finished with figures of three for 95.

Siddle (23) and Nathan Hauritz (41) kept the momentum going, the former cracking seven fours in a rousing knock before his appreciative home crowd.

Hauritz was last man out - caught by Duminy off the bowling of Paul Harris (three for 94) - just before tea.