The tourists reached the lunch interval on of 434 for four a day after the Australian captain had survived a battering from pace bowler Morne Morkel, who struck him a number of times, including a sickening blow to the back of the head.
Clarke showed admirable composure to battle it out on what is a flat wicket and having been unbeaten on 92 overnight, the right-hander was able to bring up his hundred in the second morning session, despite spending a nervy 24 balls stuck on 99.
The 32-year-old reached three figures off 215 deliveries with 11 fours as Newlands became the first overseas venue where he has two test centuries to his name.
He will resume after the interval on 137 along with Shane Watson (21), who is making his first appearance of the series after overcoming a calf problem.
The only wicket to fall in the morning session was that of Steve Smith (84), who looked in immaculate touch before playing a ball from part-time spinner Dean Elgar onto his own stumps.
It ended a fourth-wicket stand of 184 in 50 overs between Smith and his skipper.
The South African pace attack has been blunted by the absence of the world's leading test bowler Dale Steyn, who limped out of the game on Saturday with a hamstring strain. He is unlikely to bowl again in the match.
The teams are level at 1-1 with South Africa not having beaten Australia in a home test series for 44 years.


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