Steven Smith hit 77 from 100 balls, with two sixes and nine fours, to change the complexion of the match, as Australia's last three wickets added 103 runs at Headingley.
Michael Clarke hit 77 from 143 balls, including seven fours, while Ricky Ponting made 66 from 116 balls, with seven fours.
Mohammaed Aamer was Pakistan's leading bowler with 4-86.
Australia leads the two-match series 1-0.