Thisara Perera was Sri Lanka's top scorer with 25 off 29 balls including three boundaries and a six.
Seekkuge Prasanna was one of four Sri Lankan batsmen to score in double digits.
Thisara Perera also put on a 22-run partnership towards the end with Jeffrey Vandersay.
Hasan Ali once again was at his best with figures of 2 for 19 in 5.2 overs.
Pakistan's success was mainly orchestrated by Usman Khan who took his maiden five-for in just his second ODI to bowl out Sri Lanka for 103.
Fakhar Zaman and Imam-ul Haq were successful in navigating the Sri Lankan bowlers with an opening partnership worth 84 runs as Pakistan chased down the target to seal a 5-0 series sweep by nine wickets.