Pakistan were 117-4 in reply in the post-lunch session when heavy rain drove the players back to the pavilion for the second time in the day and forced the umpires to call for an early tea.
Azhar Ali was unbeaten on 47 and Sarfraz Ahmed was on 14 at the break.
Pakistan captain Misbah-ul Haq, who was slated to bat at number five, has pushed himself back in the order due to a mild groin strain suffered while fielding. But he was padded up to come in next.
Tharindu Kaushal was leg-before to left-arm seamer Rahat Ali for 18 and last man Pradeep fell in the same fashion to Yasir without scoring.
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Yasir finished with 5-78, joining his idol Shane Warne as the only overseas bowlers to claim five or more wickets in an innings three times during a Test series in Sri Lanka.
Yasir had taken 2-79 and 7-76 in the first Test in Galle to fashion Pakistan's 10-wicket win. He then claimed 6-96 and 2-55 in the second match in Colombo which Sri Lanka won by seven wickets.
Pakistan lost both their openers by the score of 40 and star batsman Younis Khan was run out off the last ball of the morning session to make it 45-3.
Left-hander Shan Masood scored 13 in his first appearance in the series when he was leg-before to Dhammika Prasad, a decision that was reviewed by the batsman and overruled by the TV umpire.
Ahmed Shehzad made a fluent 21 when Nuwan Pradeep, brought in first change in place of Suranga Lakmal, had him caught behind by Dinesh Chandimal with his third delivery.
Azhar and Asad Shafiq repaired the early damage with a 46-run stand for the fourth wicket on either side of a 19-minute interruption for rain early in the post-lunch session.
Shafiq fell in the second over after resumption for 15, playing back to a full-pitched delivery from Prasad and was given out leg-before.