Pakistan resumed at 46-1 and lost Mohammad Hafeez (11) and Ahmed Shehzad (38) in the first session.
At the break, Younis Khan was batting on 23 with skipper Misbah-ul Haq on 24, with Pakistan trailing Sri Lanka's first innings total of 204 by 83 runs.
Pacemen Suranga Lakmal and Shaminda Eranga took one wicket each.