Smith reached the interval unbeaten on 61 off 107 balls with rookie Nic Maddinson, badly needing a big score to protect his Test place, not out seven in Australia's 395 for four.
Australia added 117 runs off 34 overs in the extended morning session and were poised to take the lead during the afternoon.
Usman Khawaja was dismissed on 97 for the second time this season when he played away from his body and edged Wahab Riaz to wicketkeeper Sarfraz Ahmed.
Khawaja also missed out on a century against South Africa in the second innings of last month's first Test in Perth.
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Peter Handscomb claimed his third half-century in his three Tests to push along the Australia scoring.
He was dropped off a sharp caught-and-bowled chance by Mohammad Amir on 51, but three runs later he found Sami Aslam at point off Sohail Khan.
Handscomb, playing on his home pitch, added 92 runs with Smith off 141 balls.
Paceman Riaz continued to have problems bowling no-balls and has overstepped 12 times in the 23 overs he has bowled so far.
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