Malinda Warnapura was bowled first ball by Umar Gul and Tharanga Paranavitana was removed in similar fashion by Pakistan captain Younus Khan to make Sri Lanka 23-2.
Skipper Kumar Sangakkara, who led a charmed life while making 45, was trapped leg-before by off-spinner Saeed Ajmal with the last ball of the session as Sri Lanka went to lunch on a shaky 63-3.
Sangakkara was dropped twice on 16 and 40, both times by Khurram Manzoor in the gully region off young left-arm fast bowler Mohammad Aamer.
Mahela Jayawardene, who began by flicking his first ball from Younus to the square-leg fence, was unbeaten at the break on 10 after adding 40 for the third wicket with Sangakkara.
Sri Lanka are aiming for a clean sweep of the three-match series after winning the previous two Tests.
The tourists, who resumed at the overnight score of 289-7, lost their last three wickets in 22 balls for the addition of just 10 runs.
Left-arm seamer Thilan Thushara finished with 5-83, his maide