Saeed Ajmal took all five wickets as Pakistan finished on top on a controversial day which had the visitors in command.
South Africa were struggling at 5-139 behind Pakistan's first innings of 338 after Ajmal had finished with 5-41.
Kallis was controversially given out caught but the review showed that the ball had not touched his bat - he was then given out leg before on the advice of television umpire Billy Bowden.
South Africa 139 for 5 (Ajmal 5-41) trail Pakistan 338 (Shafiq 111, Younis 111, Philander 5-59) by 199 runs.
2nd Test, Day 2 (Cape Town), Feb 2013
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Tanvir Ahmed Sarfraz Ahmed Mohammad Irfan Philander, Vernon D Asad Shafiq Saeed Ajmal Kallis, Jacques H Peterson, Robin John Morkel, Morne Amla, Hashim M Smith, Graeme CGrounds Tagged in ClipDex
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