Younis Khan continued his superb innings with 205 not out while Asad Shafiq was one not out as Pakistan added 213 runs after resuming at 304 for two.
Younis, on 181, became the third Pakistani to complete 8,000 Test runs after Javed Miandad (8832) and Inzamam-ul Haq (8829).
Australia got only two wicket in the two sessions when they had Azhar Ali for 109 and skipper Misbah-ul Haq for 101.
Pakistan lead the two-match series 1-0 after winning the first Test by 221 runs in Dubai.