Stuart Pearce's Young Lions found themselves a goal down in the 25th minute when the visitors broke forward and Mohammad Klibat looped a shot past Ben Amos.
Martyn Waghorn equalised with a header 13 minutes after the break and a Marvin Sordell thunderbolt put England in front moments later.
A penalty from Nathan Delfouneso with eight minutes of normal time remaining and a finish from fellow substitute Henri Lansbury in injury time put the gloss on the win.
Head coach Pearce had said he would make changes from last Thursday's 6-0 European Championship qualifying triumph over Azerbaijan and only two players retained their place in the first XI, with one of them, Jack Rodwell, assuming the skipper's armband from the departed Jordan Henderson, who had been allowed to return to his club Liverpool.
Craig Dawson, scorer of two goals against the Azeri, was the other to keep his starting berth, while Amos, Andre Wisdom and Ross Barkley were the debutants amongst those to come into the team.
In total, seven of the line-up were making their first start for the Under-21s and Pearce's inexperienced side struggled to get going in the early stages.
Israel - the host nation for the 2013 Euros - looked the more dangerous, with Zion Tzemah shooting over direct from a free-kick.
Sordell saw a deflected effort bobble into the arms of goalkeeper Boris Kleyman before Or Barough went close for the visitors with a header.
Barkley unleashed a fierce effort in the 19th minute which stung the palms of Kleyman, who then punched away a free-kick from Jonjo Shelvey.
Four minutes later England were behind, Israel clearing a corner and launching a swift counter-attack which was rounded off by Klibat's curling strike beyond Amos.
It was almost 2-0 soon after when Nir Bitton drove wide, but Pearce's youngsters were inches away from an equaliser when another free-kick from Shelvey narrowly cleared the crossbar.
Dawson got on the end of a Waghorn delivery to the back post in the 41st minute but could not find the power to trouble Kleyman with his header.
Dan Gosling then nodded Shelvey's cross wide before an injury to Nathan Baker saw Steven Caulker brought on as a substitute in first half stoppage time.
Pearce made further changes at the interval, with Lansbury coming on for Rodwell and taking the captaincy, Alex Oxlade-Chamberlain introduced for Shelvey and Adam Smith becoming the latest debutant by replacing Wisdom.
England looked purposeful as the action resumed, with Sordell seeing Kleyman push one of his efforts wide and hold onto another fired in from the edge of the area.
The pressure paid off in the 58th minute as Oxlade-Chamberlain crossed from the right and Waghorn headed past Kleyman to net his second goal in successive matches.
It took just two minutes for England to score again, Sordell putting the hosts ahead in emphatic fashion by turning and lashing a shot into the corner of the net from distance.
Gary Gardner then became the final player of the evening to win his first under-21 cap for the hosts by replacing Gosling, while Delfouneso and Connor Wickham came on for Waghorn and Barkley.
Israel substitute Muanas Dabbur flashed a shot across Amos' goal, but England were firmly in control and added a third goal in the final 10 minutes, Delfouneso confidently dispatching the spot-kick after Oxlade-Chamberlain was brought down in the box.
Lansbury then wrapped up the win at the death after being fed by Oxlade-Chamberlain.
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