Junaid registered his fourth five-wicket haul with 5-51 - all coming against the same opponents - as Sri Lanka lost seven wickets in the space of 101 runs after being sent into bat on a greenish Sheikh Zayed Stadium pitch.
Skipper Angelo Mathews helped Sri Lanka's fightback with an unbeaten 57 and Shaminda Erange not out on 12, both adding 43 for the unbroken ninth wicket.
Misbah-ul Haq's decision of fielding first had looked unwise as Sri Lankan openers Dimuth Karunaratne (38) and Kaushal Silva (20) gave their team a sound start of 57 but from 66-1 at lunch, Junaid and Bhatti (3-59) changed the script in the second session.
Bhatti had Silav caught in the slip off the fourth ball after resumption and then had the experienced Mahela Jayawardene (five) caught behind in his next over. A ball earlier Jayawardene was caught behind only to see the umpire call it a no-ball.
Two balls later Bhatti had Dinesh Chandimal caught in the slip by Mohammad Hafeez for a duck to leave Sri Lanka struggling at 76-4.
It was left to Jnuaid to do the rest.
The left-armer dismissed Sri Lanka's most reliable batsman Kumar Sangakkara caught off an uppish drive at point for 16, had both Prasanna Jayawardene (five) and Sachitra Senanayake (five) both caught behind.
Mathews reached his 12th fifty with a single, having so far hit nine boundaries in his knock.
It was a different story in the first session.
Karunaratne hit three boundaries in the first three overs, and five in all, before he miscued a drive off Junaid and was smartly snapped up at gully by Asad Shafiq.
Pakistan strove hard for wickets in the first hour but wasted one review when they appealed for a caught behind against Silva off Junaid. Replays showed the batsman had not touched the ball.
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