The visitors declared their first innings on an imposing 551-6 and claimed an early wicket as Sri Lanka went to lunch on 70-1. No play was possible after lunch due to rain.
Pakistan seamer Junaid Khan started well for his team when he had opener Tharanga Paranavitana caught by Azhar Ali for a duck with the total on 11.
Khan got a delivery swinging into the left-handed batsman and the ball brushed the inside edge and flew to Ali at forward short-leg off the thigh guard.
Tillakaratne Dilshan (46 not out) and Kumar Sangakkara (22 not out) then set about steadying the innings.
Resuming day three at 488-4 after a rain-shortened second day when only 44 overs were bowled, Pakistan captain Misbah-ul-Haq scored quickly, adding 73 runs to the total in 12 overs before declaring, with the hope of beating the bad weather.
Misbah was unbeaten on 66 off 80 balls. Mohammad Hafeez top-scored in the innings with 196 while Ali scored 157. The pair added 287 runs for the second wicket.
Left-arm spinner Rangana Herath recorded the best bowling figures of 3-164 for the hosts.
Sri Lanka won the first test by 209 runs.