England all-rounder Chris Woakes took a Test-best six for 70 as Pakistan, 282 for six overnight, were bowled out for 339.
England then raced to 64 for one at lunch, with captain Alastair Cook -- dropped off Amir -- 35 not out and new number three Joe Root 23 not out.
The duo's second-wicket stand was so far worth 56 in 54 balls. But it might all have been different had Cook been out, as he should have been, on 22, with England then 38 for one.
Pakistan resumed with captain Misbah-ul-Haq 110 not out after the 42-year-old became the oldest player in 82 years to make a Test century yesterday.
But Misbah added just four runs to his overnight score, with Pakistan losing three wickets for six runs in eight balls as the quick and accurate Woakes did the bulk of the damage.
Sarfraz Ahmed made a brisk 25 but the wicket-keeper fell tamely when he cut Woakes straight to James Vince at point.
Two balls later Woakes, whose previous best was the three for nine he took against Sri Lanka at Chester-le-Street in May, bowled Wahab Riaz for a duck with an inswinger.
Misbah was then late on a Stuart Broad ball that came down the slope and was bowled to end a more than five-hour innings with 18 fours.
Amir making his return to Test cricket at Lord's -- the scene of his 2010 spot-fixing crime -- walked out to bat to a handful of boos from a capacity crowd.
He was then hit on the helmet as he ducked into a Broad delivery.
But he also hit two well-struck fours before he was last man out, caught in the slips by Root off Broad, England's senior bowler in the absence of James Anderson, ruled out with a shoulder injury. Broad took three for 71 in 27.2 overs.
Left-armer Amir opened the bowling and his third delivery swung into the middle of Alex Hales's bat for a clipped legside four.
Cook, belying his reputation as a steady run-maker, struck three fours in four balls as Rahat strayed onto the left-hander's pads. Root joined in with five fours, including a classic straight drive off Rahat.
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