Teenage left-arm quick Aamer transformed England's overnight 39 for one into 47 for five with a dramatic spell of four wickets for no runs in eight balls.
But an unbroken stand of 50 between Jonathan Trott (41 not out) and wicketkeeper Matt Prior (21 notout) saw England to 97 for five at lunch on the second day.
Pakistan, looking to square the series at 2-2 after victory at The Oval last week, did not have long to wait for a breakthrough on Friday after bad weather meant only 12.3 overs were possible on Thursday.
Aamer squared up Oval centurion Alastair Cook off Friday's third ball and the left-handed opener was caught behind for 10.
Star batsman Pietersen came in having revealed Thursday how his confidence had been "hammered" by his failure to score a Test century in 25 innings.
That sequence though was extended to 26 by a first ball nought.
Pietersen attempted to drive a ball angled across him by Aamer, and well wide of off-stump, but succeeded only in edging to wicketkeeper Kamran Akmal.
The overcast conditions were helpful to swing bowling but Aamer's success was primarily down to his own skill and England's inability to 'line him up'.
Collingwood survived a hat-trick ball from the 18-year-old but could do nothing about a full-length, late inswinger that rapped him on the pad.
Billy Bowden rejected Pakistan's lbw appeal amidst a hint an inside edge.
But Pakistan sought a referral from the Decision Review System (DRS) and, with replays indicating no edge, the New Zealand umpire reversed his verdict to leave England 39 for four.
Trott, eight not out overnight, square-drove and cover-driving Mohammad Asif for fours off Friday's 16th and 17th balls for England's first runs of the day.
But Morgan, undone by late swing from Aamer outside off-stump, found no comfort on his Middlesex home ground.
Pakistan may have dropped 18 catches this series but Yasir Hameed's recall at The Oval has improved their fielding and he made no mistake with the second slip chance.
Former Ireland left-hander Morgan's exit meant England's Nos 4, 5 and 6 (Pietersen, Collingwood and Morgan) hadn't scored a run between them.
Matt Prior might have been out for a duck too when he drove Aamer to substitute fielder Umar Amin in the gully.
But Amin wasn't sure if the ball had carried and, with replays inconclusive, Prior survived.
Aamer's initial spell on Friday, from the Pavilion End, saw him take four wickets for 11 runs in 5.3 overs with two wicket-maidens.
Meanwhile the luckless Asif produced the equivalent of a fast leg-break that did too much to dismiss Prior.
Trott, batting, with great resolution, late cut off-spinner Saeed Ajmal for four - 41 balls after his last boundary.
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