The hosts took seven for 141 in the final session to at least limit the damage after the tourists were 205 for two at one stage.
Pakistan, resuming overnight on 14 without loss in reply to Australia's meagre 127, reached 331 for nine at stumps with last pair Danish Kaneria (two) and Mohammad Asif (nought) at the crease. Imran Farhat brought up his 13th Test half-century but soon fell for 53. Salman Butt top scored for Pakistan with 71.
Faisal Iqbal (27) was the first to fall after tea – to a wonderful Shane Watson catch. He slashed at a wide delivery from Peter Siddle and Watson, back-pedalling furiously, took a terrific catch at deep point. Mohammad Yousuf (46) was next to go with the score on 236 when Brad Haddin pulled off a brilliant catch, giving Mitchell Johnson his second scalp. Umar Akmal was typically frenetic in clubbing nine fours in his 48-ball 49 before Doug Bollinger trapped him lbw. Bollinger soon had his second wicket with the second new ball as Misbah-Ul-Haq (11) edged to Haddin. He grabbed a third when Watson at deep point held onto a catch from Kamran Akmal (14) to leave the visitors 295 for seven. Umar Gul (12) and Mohammad Sami (12) also fell before the close.