David Vaughan came closest for Wales in a goalless first half but his shot hit the the post with goalkker Carson beaten.
The hosts took the lead just a minute into the second half when Newcastle United midfielder James Milner beat Lewis Price with a fiece drive.
The hosts doubled their lead with just 17 minutes remaining when Ipswich Town striker Darren Bent headed home a Stewart Downing cross.
England U21: Carson, Hunt, Johnson (Taylor 83), Davenport, Harding, Pennant (Whittingham 75), O'Neil, Milner, Downing, Cole (Bent 19), Stead. Subs Not Used: Kilgallon, Lonergan, Baines, Hinshelwood.
Booked: O'Neil.
Goals: Milner 46, Bent 73.
Wales U21: Price, Anthony, Duffy, Parslow, Gilbert, Vaughan, Jamie Tolley, Fowler (Crowell 69), Pipe, Birchall (Carpenter 76), Calliste. Subs Not Used: Davies, Morgan, Spender, Fish, Worgan.
Referee: Damien Ledentu (France).