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Ponting, who made 55 off 84 deliveries and Clarke (73 of 96 balls) lifted Australia from trouble with a 122-run third wicket stand after they lost both their openers inside the first five overs with the team score at six.
Apart from Ponting and Clarke, Cameron White (22) was the other top-order batsmen to have made notable contribution.
Dale Steyn and Robin Peterson shone with the ball for South Africa, picking up three wickets apiece giving away 21 and 45 runs respectively.
Lonwabo Tsotsobe (1/29) and Pakistan-born leg-spinner Imran Tahir (1/33) also returned among wickets for Proteas.
Opting to bat, Australia had a precarious start as Shane Watson departed in the very fourth ball, lbw to Steyn.
It could have been double blow for Australia in the first ball of the second over had Jacques Kallis not dropped Brad Haddin at short point off Lonwabo Tsotsobe.
But it was not to be Haddin`s day today as a brilliant Tsotsobe caught him short of the crease with a direct throw at the wicket.
After the early dismissals, skipper Ponting and Clarke joined hands and the duo played cautiously with occasional boundaries in between to raise the 100-run stand for the third wicket in 131 balls.
With wickets hard to come by, Proteas captain Smith brought back Steyn into the attack in the 29th over and Clarke welcomed the quickie with a pull over mid-wicket.
It was left-arm spinner Robin Peterson who broke the dangerous-looking third partnership when he had Ponting caught at long-off by Hashim Amla but not before rival skipper scored his second consecutive half-century in the practice games, coming off 84 balls with the help of seven hits to the fence.
Three overs later Peterson struck another big blow by scalping Clarke. Looking to cut a quicker Peterson delivery, Clarke edged one to AB de Villiers behind the stumps. He faced 96 deliveries en route to his fifty which was laced with six boundaries.
