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Pakistan were 60 for four at the interval as Morne Morkel took two wickets, while Vernon Philander and Dale Steyn claimed one each. Veteran Pakistan batsman Younis Khan counter-attacked for his team and was unbeaten on 24.
South African captain Graeme Smith, captaining his country for the 100th time, proved correct in his assessment of partly cloudy conditions, following early morning rain and a pitch with a tinge of green that offered good bounce.
Pakistan were bowled out for 49 in the first innings of the first Test, which South Africa won by 211 runs, and openers Mohammad Hafeez and Nasir Jamshed started cautiously, scoring just 10 runs before left-hander Jamshed was caught behind off Philander for three.
He had survived a chance to Faf du Plessis at gully off the previous delivery.
Hafeez then edged Steyn to first slip after making 17 before the tall Morkel took two wickets in an over, having Azhar Ali caught behind attempting an extravagant drive.
Pakistan captain Misbah-ul-Haq followed, caught at short leg off a sharply rising delivery.
That left Pakistan reeling at 33 for four but Younis showed a willingness to play attacking strokes as he and Asad Shafiq added 27 runs without further loss before lunch.