Following defeats to Italy and Norway the Young Lions were already eliminated from the competition but Ofir Kriaf's 80th minute curling effort from the edge of the penalty area ensured they would finish bottom of Group A.
With nothing but pride to play for boss Stuart Pearce - whose future is also in doubt following the disappointing tournament - opted to make several changes to his starting XI.
Liverpool's Andre Wisdom captained the side while the likes of Jason Steele, Nathaniel Clyne, Tom Lees and Josh McEachran were all handed starts at the Teddi Stadium.
Tournament hosts Israel still held faint hopes of reaching the semi-finals, but needed a convincing win as well as a big victory for Italy against Norway in the other group game to be within a chance of going through.
We had to wait until the 20 minute mark to get the first effort on target, Sintayehu Sallalich's cross shot from a tight angle pushed away by goalkeeper Steele.
The best opening in the first half though went England's way on 33 minutes, Israel goalkeeper Boris Klaiman doing well to save from Tom Ince's shot and Wilfried Zaha's header in quick succession.
Pearce's side began the second half well with Connor Wickham - who had previously seen a number of shots well blocked - bending in an effort that fizzed just wide of the right-hand post.
Nir Biton then got the crowd to their feet with a swerving effort from distance on 57 minutes that beat Steele but thumped off the crossbar and rebounded away from danger.
The game then deteriorated and looked to be meandering to a draw before Kriaf's late intervention, completing what has been a miserable tournament for Pearce's young charges, who failed to score a goal from open play.