Tries from flanker Tom Rees and skipper Chris Bell, plus a penalty and conversion from fly-half Adrian Jarvis gave England an early lead they were never to relinquish.
Wales were unable to recover despite wing Matthew Nuthall scoring two fine tries.
The Welsh youngsters also had two scores disallowed, as centre Steve Ireland's effort was brought back for an earlier infringement, while wing Chris Czekaj was denied by a marginally forward pass.
England led 15-7 at half-time after Nutthall's first score, converted by full-back Matthew Jones, gave Wales hope.
A second try for the Cardiff Blues flier followed soon after the restart, but England pulled away again when substitute Geoff Parling was rumbled over from a lineout and Jarvis struck his second penalty.
Fly-half Nick Macleod jinked his way over for a converted try to bring Wales back to within four points.
Then Nuthall came desperately close to scoring a third try to claim the victory for Wales, but it was England who claimed fifth place as a third penalty goal by Jarvis sealed the result.
Wales U21: M Jones; M Nuthall, G Evans, S Ireland, C Czekaj; N Macleod, R Rees; J Yapp, K Crawford, C Griffiths, A Wyn Jones, I Evans, T Brown, J Edwards, G Quinnell.
Replacements: D Maddox, W Kay, J Mills, R Dale, J Ireland, A Bishop, L Andrews.
England U21: L Myring; H Barratt, C Bell (capt), A Reay, M Garvey; A Jarvis, C Stuart-Smith; N Wood, S Friswell, T Warren, J Percival, C Day, L Narraway, T Rees, R Thorpe.
Replacements: C Dott, A Croall, T French, G Parling, C Goodman, J Bedford, J Bailey.