England won the toss and chose to bat but went from 110-2 to 184 all out as they were dismissed in 40.2 overs.
Daniel Bell-Drummond top-scored with 51 but it was in vain as England went 3-0 down in the five-match series.
Sri Lanka A reached their target in 37 overs as Shehan Jayasuriya followed up his 5-35 with a knock of 83.
England Lions have lost their one-day series against Sri Lanka A after being beaten by four wickets in the third ODI in Kurunegala.