He is playing his first tournament since suffering serious injuries in a car accident in December 2022 that kept him out of last year's IPL as well as the 50-overs World Cup in India
Sri Lanka, chasing 362 for victory, went from 32 for no wicket to 78 for one between the showers but neither side had any chance of forcing victory and England won the series 2-0.
England fast bowler James Anderson trapped Kaushal Silva lbw for 16 with an excellent inswinging delivery to claim the only wicket.
Dimuth Karunaratne finished unbeaten on 37 with Kusal Mendis on 17.
Mendis hit the last ball of the match by Joe Root for six before the rain returned.