Younis Khan smashed his third hundred in consecutive innings and was unbeaten on 111 after Pakistan won the toss and batted on a flat Sheikh Zayed Stadium pitch.
The other unbeaten batsman was Azhar Ali on 101.
Pakistan lost openers Ahmed Shehzad (35) and Mohammad Hafeez (45) in the two sessions.
Pakistan, leading the two-match series 1-0, remained unchanged from the side which won the first Test by a big 221-run margin in Dubai.
Australia, seeking to avoid their first series defeat against Pakistan since 1994, made two changes with Glenn Maxwell and Mitchell Starc replacing Steve O'Keefe and Alex Doolan.