Openers Khurram Manzoor (14) and Ahmed Shehzad (five) were at the crease as Pakistan trail by 409 runs.
Dilruwan Perera missed a century on his debut by five runs while skipper Angelo Mathews missed his second in the series by nine as Sri Lanka frustrated Pakistan who had looked for early wickets after Sri Lanka resumed the day at 220-5.
Paceman Junaid Khan had figures of 3-81 while Mohammad Talha took 3-99. Spinner Saeed Ajmal finished with 2-120.
Sri Lanka lead the three-Test series 1-0 after winning the second Test in Dubai by nine wickets. The first Test ended as a draw in Abu Dhabi. (AFP)