The Arsenal right-back struck on 12 minutes when he blocked a clearance from keeper Boy Waterman and lifted the rebound beyond the grounded stopper.
Julian Jenner wasted a chance in each half for the hosts in a dour match in which England were rarely troubled.
Hard-working Preston striker David Nugent dragged an early shot wide and Peter Whittingham went close late on.
Stand-in Under-21 coach Sammy Lee
"When you have a performance like that it gives everyone encouragement, when you get something like that the youngsters can think 'yeah, we have got something coming up, we can step up and move on'.
"It only bodes well for the future of English football.
"There's a good nucleus of players who wouldn't embarrass themselves if they stepped up (to the senior team).
"It's good for Steve McClaren that he call on them whenever he feels fit. That's a credit to the depth of English football."
Holland U21: Waterman, Tiendalli (Vermeer 63), Donk, Van Der Struijk (Koenders 46), Drenthe (De Jong 63), Schilder, Jenner, Kruys (Agustien 46), MacDonald (Brama 57), Bakkal (Elia 57), Owusu-Abeyie.
Subs Not Used: Zuiverloon.
England U21: Carson, Hoyte, Baines (Rosenior 46), Davies, Kilgallon, Huddlestone, Routledge (Welsh 78), Milner (Whittingham 65), Nugent (Onuoha 85), Young, Walcott (Jerome 83).
Subs Not Used: Camp.
Goals: Hoyte 12.