The 16-year-old – who has been a mainstay in the Magpies’ Under-18s side this season – started for the Young Lions in Bijeljin, Gradski.
And after just quarter of an hour, Gibson gave his side the lead when he met Nya Kirby’s corner to convert what turned out to be the only goal of the game.
Gibson – the younger brother of United Under-23s’ full back Liam – played the full 90 minutes for his country as they rounded off the Elite Round qualifiers with another win.
The Young Lions’ wins over the Czech Republic and Slovenia earlier this month had ensured their qualification for the May’s finals in Croatia.
Meanwhile forward Adam Armstrong, who is currently on loan at Barnsley, made a second half substitute appearance as England Under-20s won the Four Nations tournament with a 2-0 victory over Senegal in France.
Former Magpies coach Paul Simpson’s side won it thanks to goals from Dominic Calvert-Lewin and Dominic Solanke early on at the Stade Municipal Du Haut-Champ in Ploufragan.
And Armstrong, 20, came on for Patrick Roberts after 66 minutes as England saw out the game to win the tournament.
Goalkeeper Freddie Woodman, who is on loan at Kilmarnock, was an unused substitute in that win over Senegal, while fellow stopper Matz Sels didn't come off the bench in Belgium's 3-3 friendly draw with Russia in Sochi.
And winger Florian Thauvin, on loan at Marseille, was also an unused substitute as his France side beat Spain 2-0 in a friendly at the Stade de France.