Pacers Suranga Lakmal and Shaminda Eranga took a wicket each as Pakistan reached 121/3 at lunch in reply to Sri Lanka's first innings total of 204.
At the break, Younis Khan was batting on 23 with skipper Misbah-ul-Haq unbeaten on 24 as Pakistan trailed by 83 runs.
Resuming at 46/1 Pakistan lost Mohammad Hafeez (11) and opener Ahmed Shehzad (38) to irresponsible shots, which gave Sri Lanka the semblance of a chance to restrict Pakistan.
Hafeez had started off well, hitting two straight boundaries off Lakmal before miscuing a drive off the same bowler and was smartly caught at short cover by Kaushal Silva.
Silva, also a wicket-keeper but selected as opener in this Test, dived to his left and caught the ball inches from the ground.
Shehzad also miscued a hook shot and was caught at forward square-leg by Dimuth Karunaratne after hitting three boundaries.
Both Misbah and Younis batted sensibly with Pakistan's hopes of a big lead resting on their shoulders, adding 38 for the unbroken fourth wicket stand.
The second Test will be played in Dubai (January 8-12) and the third in Sharjah (January 16-20).