Holland made the most of a disjointed performance by England to claim a comfortable friendly win.
Holland's Frank Van Mosselveld (l) challenges John Welsh
Fulham striker Collins John put the Dutch ahead when Liam Ridgewell failed to cut out Edson Braafheid's cross.
Edridge Joger made it 2-0 before half-time when he rose unchallenged at the far post to head Stijn Schaars' deep free-kick past Scott Carson.
Substitute Leroy Lita did manage a consolation for England by turning in a John Welsh cross in the final minute.
Both sides were intent on attacking in the opening stages, but it was the Dutch who were looking more threatening in front of goal.
Stijn Schaars fired over a free-kick from the edge of the penalty area and Raymond Fafiani volleyed wide
England were living dangerously, and their resistance only lasted 19 minutes.
John found the net from close range after Ridgewell failed to deal with Braafheid's dangerous cross from the left.
That at least served to settle England down and they had three chances to reply in quick succession around the half-hour mark.
First Holland goalkeeper Boy Waterman failed to deal with a free-kick and the ball fell to Liam Ridgewell, but his shot on the turn was deflected wide by John's outstretched leg.
Soon after Carlton Cole's cross was volleyed over at the far-post by Milner, then Waterman had a clearance charged down by Cole and was only just able to clear his lines.
But Peter Taylor's side fell further behind on 37 minutes when a deep free-kick was sent towards the far post and Joger found space to nod downwards into the net.
England made three substitutions at half-time with Lee Camp replacing Carson in goal and Kieran Richardson and John Welsh coming on for Leighton Baines and Dean Ashton.
But the Dutch picked up where they left off, forcing Camp into two smart saves from Fafiani and John within five minutes of the restart.
England's best chances were coming on the break and Jon Stead should have done better when he was sent clear by Richardson.
Milner also sent a shot skidding just past Waterman's post from outside the area before Welsh went close from long range as Taylor's side pressed for a consolation.
And the late pressure paid off as Lita pounced on to Welsh's cross to prod the ball past Waterman from close range in the 90th minute.
England U21: Carson (Camp 46), Hoyte (Lita 65), Baines (Welsh 46), Huddlestone, Taylor, Ridgewell, Routledge (Marney 70), Whittingham, Cole (Stead 41), Ashton (Richardson 46), Milner.
Subs Not Used: Harding, Watson, Carter, Lonergan.
Booked: Marney, Stead.
Goals: Lita 90.
Holland U21: Waterman, Verhaegh, Wolfgang (Maduro 77), Van Mosselveld, Braafheid, Schaars, De Ridder, Fafiani (Tuyp 85), John, Hofs, Joger (Korf 83).
Subs Not Used: De Zeeuw, Pasveer, Van Der Struyk.
Goals: John 19, Joger 37.
Ref: Darko Ceferin (Slovenia).