Dimuth Karunaratne, Avishka Fernando star as visitors snap losing run in rain-affected second ODI.
The first ODI between Scotland and Sri Lanka in Edinburgh on Saturday was abandoned without.
Rain and Rahmat Shah foil Scotland despite Calum MacLeod hundred, take series 1-0.
Kyle Coetzer 74 helps Scotland beat Ireland by six wickets in Friday in Quadrangular T20 Series game in Oman.
Toby Bailey suffered a debut defeat as interim Scotland head coach in the opening T20 Quadrangular Series match against the Netherlands in Oman.
Scotland are set to host Sri Lanka for two one-day international games on 18 and 21 May next year.