Former Arsenal midfielder Hayden was deployed in an unfamiliar right back role for the clash at Southampton's St. Mary's Stadium, but turned in a solid display as Aidy Boothroyd's youngsters prevailed thanks to a last-minute strike from Jack Stephens.
Twenty-one-year-old Hayden played the full 90 minutes for the Young Lions. Demarai Gray and Lewis Baker scored England's other two goals.
Also on Thursday, goalkeeper Freddie Woodman started between the sticks for England Under-20s in their second game of the Continental Cup in South Korea.
And though he played the full game, the 19-year-old was unable to prevent Paul Williams' side from slipping to a 2-1 defeat to the tournament hosts.
England, who beat Nigeria 8-1 on Wednesday, led through Ovie Ejaria, but Youhyeon Lee's brace won it for South Korea.
Meanwhile, two young Magpies faced each other in Mjava as Lubo Satka's Slovakia Under-21s faced Kyle Cameron's Scotland Under-21s.
And it was Satka's side who prevailed, winning the friendly 4-0. Cameron - who is currently on loan at Newport County - was replaced after 71 minutes for the Scots.
On Wednesday, goalkeeper Matz Sels was an unused substitute for Belgium as they drew 1-1 with Holland at the Amsterdam ArenA.