England began the game like a house on fire and took the lead in the fifth minute when Arsenal wonderkid Max Dowman went on a mazy run, before superbly firing into the corner from a very tight angle.
The in-form Alejandro Gomez Rodriguez bagged his fourth goal of the tournament when he calmly slotted home 10 minutes later.
Harry Howell bent in a superb effort from 15 yards eight minutes before the break, before Harry Gray pounced on a howler from Czech goalkeeper Adam Paar three minutes later.
The Czechs improved after the interval and grabbed a consolation just before the hour mark when Martin Palascak's header nestled in the far corner.
Gray and Rodriguez spurned good opportunities to put more gloss on the scoreline, and that came back to haunt them when Hugo Sochurek volleyed in one minute from time.
That meant their goal difference was one worse than second-placed Belgium, who lost 2-1 to group winners Italy. England are now out of the competition after picking up a win, a draw, and a loss apiece.