Hafeez, who was reported for a suspect action during the preceding Test series and underwent tests in Chennai last week, took the field only because he is allowed to play till the results are declared.
The 34-year-old off-spinner seized the opportunity to finish with his best one-day figures of four for 41 after Pakistan captain Azhar Ali won the toss and elected to field.
Dinesh Chandimal top-scored with an unbeaten 65 off 68 balls as the Sri Lankans struggled to come to terms with the accurate Pakistani bowling.
Opener Tillakaratne Dilshan made 38 after being caught off a Mohammad Irfan no-ball when he was on two.
Seamer Rahat Ali took two wickets in the 49th over as Sri Lanka scored 56 runs in the last nine overs.
Ninth-ranked Pakistan need to win the five-match series to stay in contention for a place in the eight-nation Champions Trophy in England in 2017.
Sri Lanka, currently ranked fifth, are assured of taking part in the tournament.
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