Kaushal Silva was unbeaten on six and Kumar Sangakkara on five, with five sessions left in the match at Sharjah.
Earlier today, Pakistan were bowled out for 341 in their first innings, 87 short of Sri Lanka's first innings total of 428 for nine declared.
Skipper Misbah-ul Haq scored 63 to notch up his 24th Test half-century before holing out to left-arm spinner Rangana Herath who finished with 5-125.
But it was paceman Shaminda Eranga who brought Sri Lanka early success after Pakistan resumed on 291-6 and looked for quick runs to force a result and level the series.
Misbah struck Herath for a six and then took a single to complete his fifty off 86 balls. He hit three sixes and a four before being caught at long-on.
Junaid Khan also struck two boundaries to reduce the deficit before he too was caught in the deep off Herath.
Sri Lanka lead the three-match series 1-0 after winning the second Test in Dubai by nine wickets.
The first Test in Abu Dhabi ended in a draw.
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