Australia were 494 for seven when rain brought an early tea.
Part-time off-spinner JP Duminy claimed Test-best figures of four for 73, taking three wickets after lunch as Australia went for quick runs.
Australia added 103 runs for the loss of Steve Smith's wicket on a chilly, windy morning and added another 60 runs in 13.4 overs after lunch before rain stopped play.
With strike bowler Dale Steyn out of action after suffering a hamstring injury on the first day, the key for Australia was to prevent the South African bowlers from making a breakthrough early in the day with an almost-new ball.
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It finally came with a cover drive for four off Philander. He had faced 215 balls and hit 11 fours.
Smith, meanwhile, played some aggressive strokes as he made 84 in a fourth wicket stand of 184 with Clarke before he chopped a wide delivery from part-time left-arm spinner Dean Elgar into his stumps. He hit nine fours and three sixes in a 155-ball innings.
In trying to hit Duminy for a fourth six he mistimed a shot to long-off.
Brad Haddin also perished playing an attacking shot and Mitchell Johnson was caught down the legside first ball by wicketkeeper AB de Villiers off Duminy.
Clarke, who had gone 11 Test innings without making more than 24 runs, batted with increasing confidence and reached 150 for the tenth time in his career off 288 balls when he clipped Abbott for his 17th four.