At lunch on Friday, England were 110 for three after Alastair Cook was caught and bowled low down off the last ball before the break for 23, following a leading edge, by Umar Gul.
Kevin Pietersen, who like Cook was fortunate not to be given out caught behind when in single figures, was 17 not out.
England, 1-0 up in the four-match series, had made a brisk start but were pegged back when openers Marcus Trescothick (28) and Andrew Strauss (36) both fell with the score on 67.
After captain Strauss won the toss and elected to bat, England dominated the first hour.
But paceman Mohammad Sami, who'd been wayward early on, struck in the first over after the drinks break when, having switched to the Kirkstall Lane End, he took a juggling caught and bowled chance to get rid of Trescothick after the left-hander was early on an intended drive.
The Somerset batsman, who had now gone eight innings without a fifty, had looked in good touch with six fours.
And four balls later fellow left-hander Strauss exited when he edged recalled fast medium-bowler Shahid Nazir, playing his first Test in seven years, to Younis Khan at second slip.
Strauss had also looked in fine form with five fours but Nazir, who'd beaten the bat consistently without threatening a wicket, now had impressive figures of one for five in five overs.
And the 28-year-old was unlucky not to have Pietersen, on two, caught behind by wicket-keeper Kamran Akmal with England 77 for two in the 19th over.
Veteran Australian umpire Darrell Hair turned down the appeal but replays suggested Pietersen had inside-edged the ball on to his back leg.
Five runs later Cook, on eight, also had a lucky break when West Indian umpire Billy Doctrove failed to detect an inside edge off Sami well caught by a diving Akmal.
Strauss had earlier decided to bat despite the overcast conditions which usually assist swing bowling at Headingley.
Trescothick, to the sixth ball of the day, off-drove Sami for four and Strauss, also off Sami, later square-cut a short ball outside off-stump through point for four and then clipped a legside delivery to the mid-wicket fence.
In the ninth over Nazir, in for the dropped Abdul Razzaq, came on for his first bowl in Test cricket since appearing against Sri Lanka at Lahore in 1999.
None of Pakistan's bowlers had the pace to escape with bowling short and when Gul pitched the ball half-way down the pitch he was twice pulled, in front of square, for four in consecutive deliveries by Trescothick.
Strauss's flashing square-cut off Gul over gully brought up a fifty stand with Trescothick in 12 overs as England made brisk progress.
England made one change to the team that won the second Test by an innings and 120 runs at Old Trafford with Chris Read in for dropped wicket-keeper Geraint Jones, whose run of 31 consecutive Tests since April 2004 was ended by the selectors because of a lack of runs.
Pakistan made three changes with Salman Butt, dropped at Old Trafford, restored as an opener in place of the injured Imran Farhat (right ring finger) while all-rounders Razzaq and Shahid Afridi were dropped.
Specialist opener Taufeeq Umar came in for his first game of the series as Akmal, who opened at Old Trafford, moved back down the order.