They led 13-0 at halftime, having opened the scoring with a converted try by Nathan Earle of Saracens, one of eight new caps in the starting XV.
A try by Australian Adam Ashley-Cooper put the Barbarians back in contention but Earle's club mate Nick Isiekwe went over to extend the lead to 23-7 before a late try by Samoan Joe Tekori.
Danny Care crossed the line to have the last word for England.
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Head coach Eddie Jones's side are preparing for a two-match test series in Argentina, on 10 June and 17 June.
(Reporting by Steve Tongue)
