It took Pakistan just four balls to strike, with Rory Burns lbw for four to towering left-arm paceman Shaheen Afridi on the second day.
England captain Joe Root was still on nought when he was given out leg before to Afridi but a successful review spared the skipper.
Pakistan were soon celebrating again, however, when Mohammad Abbas had Dom Sibley lbw, the batsman wasting a review when clearly out.
But there was no need for the third umpire to get involved when Abbas bowled left-handed batsman Stokes for a seven-ball nought with a superb delivery that clipped the top of off-stump.
That left England 12-3 inside six overs.
Pakistan made 326 all out in their first innings, opener Shan Masood top-scoring with a Test-best 156.
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