Misbah missed his sixth Test hundred by a mere three runs but a career best 70 not out by Sarfraz Ahmed and a defiant 32 by Bilawal Bhatti kept Pakistan's fight to take them to 330 for seven at close on a cloudy day.
When bad light and drizzle ended play 15 overs before schedule, Saeed Ajmal was on seven and Pakistan were leading by 107 runs with a full day's play remaining.
Sarfraz added an invaluable 67 runs for the seventh wicket with Bhatti to frustrate the Sri Lankan bowlers who bowled with discipline and patience on a pitch which had little response for bowlers.
Sri Lanka will look for an early wrap up of Pakistan's second innings to take a 1-0 lead in the three-match series after the first Test ended in a draw in Abu Dhabi last week.
The third and final Test will be played in Sharjah from Thursday.
Sri Lanka have never defeated Pakistan by an innings in the 44 previous Tests between the two nations. The first Test in the three-match series ended in a draw in Abu Dhabi last week.
Earlier, Pakistan had resumed on their overnight score of 132-3. They needed Younis and Misbah to dig deep, but Younis tried to drive a slightly wide delivery from Lakmal, managing only to edge it to wicketkeeper Prasanna Jayawardene, who held his eighth catch of the match.
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