Shafiq, who survived a close lbw call off paceman Vernan Philander after the original out decision was reversed on review, will resume on 67 not out.
He and skipper Misbah (60 not out) have put on 128 runs for the fifth wicket, the second highest partnership of the match.
South Africa opted to take the new ball four overs before lunch and immediately the wicket came to life with movement and bounce. How they use it in the afternoon session is likely to be key to the remainder of the day's play.
Pakistan lead the two-match series 1-0 and have put in a much better batting display in their second innings having been skittled for 99 on the opening day. South Africa then raced to 517 to put themselves in position to tie the series.
(Reporting by Nick Said in Cape Town; Editing by John O'Brien)
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