With Abendanon making over a hundred metres running with ball in hand, and replacement wing Jonny May showing searing pace, England were an attacking threat throughout, although defensive lapses early in the second half allowed the Barbarians back into the game.
May expertly finished two tries in the 63rd and 70th minutes which settled the contest after the Barbarians had scored twice after half-time to close the gap to 24-31.
The 22-year-old May, who only arrived in South Africa last weekend as a replacement for George Lowe, came off the bench in the 26th minute after Ugo Monye injured himself in a tackle which knocked him out and damaged his neck.
Monye went to hospital for a scan, but England management are confident there is no serious damage to his neck.
Abendanon, himself a late call-up to the tour party, scored in the 19th, 32nd and 36th minutes.
Flyhalf Charlie Hodgson, who dominated the territorial battle with his boot but also sparked his backline well, missed just one kick at goals as he added seven conversions and a penalty.
Eighthman Ben Morgan and centre Anthony Allen were the other England players who scored tries, while the tourists were also awarded a penalty try in the last minute.
The Barbarians, drawn from B Division provinces, were thoroughly outplayed except in the third quarter, when scrumhalf Shaun Venter scored twice in three minutes.
SA Northern Barbarians – Tries: Joubert Engelbrecht, Shaun Venter (2), Deon Scholtz. Conversions: JC Roos (4). Penalty: Roos.
England – Tries: Nick Abendanon (3), Ben Morgan, Jonny May (2), Anthony Allen, penalty try. Conversions: Charlie Hodgson (7). Penalty: Hodgson.