Sri Lanka, who resumed after lunch at 147-3 in reply to Pakistan's modest 138, lost three wickets in the post-lunch session on the second day to go to tea at 231-6.
Skipper Angelo Mathews was the last recognised batsman at the crease on 57, and Dhammika Prasad was on 13, with Sri Lanka just 93 runs ahead and four wickets in hand.
Yasir, whose seven-wicket haul in Sri Lanka's second innings fashioned Pakistan's 10-wicket victory in the first Test in Galle, once again tormented the rival batsmen.
He had Lahiru Thirimanne caught at short-leg by Azhar Ali for seven before lunch, and then bowled both Dinesh Chandimal (one) and Kithuruwan Vithanage (three) on resumption.
Yasir yorked Chandimal with a faster delivery and Vithanage fell to an ungainly reverse sweep, failing to connect bat to ball.
Opener Kaushal Silva, who hit a century in Galle, once again proved his team's star performer with a solid 80.
Silva and Mathews put on 72 for the fourth wicket to take the score to 191-3 when three wickets crashed in the space of 11 runs to open up the tail.
Silva was run out when he drove Zulfiqar Babar to mid-on and charged down the wicket for a sharp single, only for Mathews to send him back.
Kumar Sangakkara, who resumed on 18 at the team's overnight score of 70-1, made 34 when he attempted a big hit off left-arm spinner Babar and was caught at long-on by Asad Shafiq.
Sangakkara, 37, has still not responded to media speculation that he will retire after playing the first two Tests against Pakistan and one against India in August.
Pakistan missed pace spearhead Wahab Riaz, who did not take the field on the second day after being ruled out for the rest of the series due to a fracture in the left hand sustained while batting on Thursday.
The third and final Test is scheduled to start in Pallekele from July 3.