Silva, who hit 81 in the drawn first Test in Abu Dhabi, was soildly batting on a career best 92 and with him Mahela Jayawardene unbeaten on 50 as the two took their unbroken fourth wicket stand to 127 to give Sri Lanka a lead of 50 runs over Pakistan's first innings total of 165.
The duo ensured Sri Lanka overcome a disappointing start to the day after they lost Kumar Sangakkara (26) and Dinesh Chandimal (12) in the space of 13 runs.
Sri Lanka were 132-3 at lunch and added 83 runs without losing a wicket in the second session, leaving Pakistan captain Misbah-ul Haq frustrated in his search for wickets.
Silva pulled off-spinner Saeed Ajmal to mid-wicket boundary to reach his second Test half-century and then had two fours off Ali to help Sri Lanka overhaul Pakistan's total.
Jayawardene, who failed in both the innings of the first Test with five and nought, successfully overturned a leg-before decision against him by Australian umpire Bruce Oxenford when on 26. Television replays showed Ali's delivery was pitched outside the leg-stump and was missing the off-stump.
Resuming at 57-1, Sri Lanka had hoped experienced batsman Sangakkara would score more but the left-hander fell in the sixth over of the day.
Left-arm paceman Ali, who went wicketless in the first Test, trapped Sangakkara leg before with a ball that kept straight and missed the forward push.
Junaid, who had figures of 2-47, then had Chandimal caught at deep fine-leg off an uppish hook shot.
Ajmal, also wicketless in the second innings of the first Test, once again toiled hard, having so far failed to make an impact in his 19 overs.
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