Sri Lanka was scheduled to resume at 44-3 after Thisara Perera's 4-63 had helped the home team dismiss Pakistan for 226 in the first innings.
Sri Lanka leads the series 1-0, but Pakistan left-arm fast bowler Junaid Khan ripped through its top order late Sunday by removing Dinesh Chandimal (8) and Kumar Sangakkara for duck in space of four balls.
Recalled paceman Mohammad Sami then trapped captain Mahela Jayawardene (12) lbw in the last over of the day on a wicket which has plenty of lively grass to suit the seamers.
Sri Lanka has not won a test series since 2009.