Dinesh Chandimal and Dilruwan Perera helped Sri Lanka to get a crucial 80-run lead in the first innings.
Nuwan Pradeep and Bhanuka Rajapaksa steer the visiting side to a comfortable win.
Sri Lanka have already named a depleted squad for this tour.
Both the players decided not to travel Pakistan citing security concerns.
Playing in front of home crowd and winning the Man of the Match award is a dream come true - Sohaib Malik
It was a big moment for the hosts and the victory was just a perfect icing on the cake.
Definitely, emotions will be riding high and this game will be a lot more than just cricket.
An emphatic all-round performance helped the hosts win the game by 2 wickets and they also materialized skipper Sarfraz's dream to lift the trophy in Lahore.
Pakistan got to the 103-run target with 16 balls to spare and took a 1-0 lead in the 3-match series.
Just when people thought the Lankan Lions are getting back on track, Pakistan gave them a rather harsh reality check in the ODI series.