Steven Smith scored his 17th Test hundred, fourth of 2016.
Usman Khawaja was denied the chance to score a century as Wahab Riaz dismissed him early in the morning session for 97.
Peter Handscomb survived a hostile spell from Amir early on to settle in and keep his skipper good company.
Under-fire Nic Maddinson steered clear of another low score and got his eye in, but was dismissed by Yasir Shah for 22 runs.
Handscomb scored a half-century but fell, against the run of play, for 54 to Sohail Khan.
With the sun beating down, Steven Smith took charge and made the most of the conditions and dominated the Pakistan bowlers.
Right after Australia took a 22-run run lead, bad light forced an early end to the second session. Thunder showers came about soon, abandoning the final session of play without a ball being bowled.