James Trafford, Taylor Harwood- Bellis and Cole Palmer all featured as Lee Carsley’s side made it four wins from four and are yet to concede a goal.
Newcastle United’s Anthony Gordon scored the only goal of the game on 34 minutes as he side-footed Morgan Gibbs-White’s low cross from eight yards.
Trafford – unbeaten in more than six hours at the tournament – produced a string of fine saves and was much the busier of the two keepers, particularly after the break when the young Lions were clinging on at times.
Skipper Harwood-Bellis had his hands full with a lively and inventive Portuguese, and the City defender made several timely interventions as the pressure increased towards the end of the game.
Trafford picked up a yellow card for time-wasting and Palmer came on as a sub on 74 minutes to help see England over the line.
Israel – who England have already beaten 2-0 in the group stages – now await Carsley’s side in Wednesday’s semi-final.
Tommy Doyle was an unused sub on the night.