Azhar Ali scored 52 runs from 96 balls with the help of eight boundaries before being caught by Tharindu Karunaratne from the bowling of Nuwan Pradeep.
Openers Shan Masood and Ahmed Shehzad scored 13 and 21 runs while Asad Shafiq made 15 runs and Captain Misbah-ul-Haq was out after scoring just six runs.
Ehsan Adil was dismissed for a duck.
Earlier, Sri Lanka were dismissed on 278 runs with Yasir Shah taking five wickets again.
