In his first game as Pakistan captain, Salman Butt made 45 from 68 balls, including eight fours, while fellow opener Imran Farhat hit 43 from 84 balls, with five fours, helping Pakistan to a lead of 60.
Shane Watson took 2-12 before bad light brought play to a premature end.
Earlier, Pakistan produced a devastating bowling display, with Mohammad Aamer taking 3-20, Mohammad Asif 3-30 and Umar Gul 2-16 as Pakistan skittled the Australians for their lowest score since 1984 — and their lowest ever at Headingley.
Tim Paine's 17 was Australia's top score.
Australia captain Ricky Ponting won the toss and decided to bat despite the overcast conditions, a decision he was quickly made to regret.
After a relatively innocuous start which saw Australia reach 20 without loss, Pakistan took 6-40 from 101 balls before lunch.
Aamer broke through with the first ball of the seventh over, hitting Simon Katich on the pads.
Rudi Koertzen, umpiring a test for the final time in a 17-year career, took a characteristically agonizing length of time to raise his finger, before giving Katich lbw for 13.
Before a run had been added opener Shane Watson perished in the next over, lbw to Asif for 5.
Gul then produced a superb delivery to rip out Michael Clarke's off and middle stumps, bowling him for 3 in the 13th.
Ponting made just 6 before he was lbw to Asif in the following over, and in the 17th Gul removed Michael Hussey for 5.
Gul conjured a delivery that swung so sharply television replays suggested it would have missed the stumps after pitching in line and hitting Hussey's pads, but Koertzen again raised his finger.
Butt perhaps surprisingly then handed the ball to Umar Amin, but the move was vindicated when Amin took a wicket with just his 11th ball in test cricket, as he had North caught behind in the 23rd over.
Aamer took wickets with the first two balls of the afternoon session, first removing Steven Smith's middle stump for 10, then bowling Mitchell Johnson for a golden duck.
Ben Hilfenhaus survived the hat-trick ball, but was run out by Amin in the 33rd over.
Paine played a cut shot to third man, but as they chased a third run Hilfenhaus was short of his ground by millimeters, after Kamran Akmal gathered Amin's throw.
Hilfenhaus was given out by the television umpire and the innings was ended when Paine was caught behind off Asif with the first ball of the 34th over.
Pakistan reached the tea interval just 24 runs behind and after a brief delay for rain, advanced to 75-0 in the evening session when Hilfenhaus dropped a sharp chance off his own bowling from Butt, who was on 42, in the 18th over.
Hilfenhaus quickly atoned with an inswinger that bowled Butt on middle stump in his next over, but as batting conditions improved the bowlers grew exasperated.
Farhat and Azhar Ali put on 53 for the next wicket, before Farhat was lbw to Watson in the 33rd over.
Watson then removed Ali, who fell for 30 to an excellent diving catch by Australia wicketkeeper Paine.
With the light deteriorating Ponting brought on his spinner, Steven Smith, to bowl the 39th over.
Umar Akmal duly smashed him back over his head for the first and only six of the day, before play was abandoned for bad light with 15 overs remaining.