At the close, opener David Warner was unbeaten on 16 and nightwatchman Nathan Lyon was on one as Australia still trail by 548 runs with nine wickets in hand.
Younis Khan hit an epic 213 for his fifth double hundred while Misbah-ul Haq made 101 and Azhar Ali 109.
Mitchell Starc was the best Australian bowler with 2-86.
Pakistan lead the two-match series 1-0 after winning the first Test by 221 runs in Dubai.