The Young Lions made it three wins from three at the Toulon Tournament as a pair of penalties fired them past Japan and into the last four.
Thursday's demolition of Cuba had already sealed a semi-final spot, but this victory – secured thanks to goals from George Hirst and Martell Taylor-Crossdale – maintained England's 100 per cent record.
Coach Neil Dewsnip made a number of changes for the fixture, rotating his squad, handing Luke Bolton who his first start in a Three Lions shirt.
The game began on a sombre note, with both teams pausing to pay tribute to those affected by the terror attack in London the previous night.
The Samurai Blue had further early chances, but they would come to haunt them. On the 25th minute, Daniel Kemp was brought down as he sought to collect a pass from Bolton, allowing Hirst to convert his fourth goal of the tournament.
The second half began with Japan restricted to half-chances until substitute Mizuki Ando broke free on the left before driving the ball across goal and inside the far corner to level.
Japan nearly took the lead a few minutes later as another substitute, Hiroki Abe, saw his attempt parried away by Balcombe.
The Young Lions were back in front just eight minutes from time, though, as Demetri Mitchell's foraging run was brought to a premature end in the box, with Taylor-Crossdale stepping up to score his second penalty in as many games.
The semi-finals of the competition take place on Thursday and the faultless Young Lions will wait in suspense over the next few days to find out who their opponents will be.
England Under-20s: 13 Ellery Balcombe (Brentford), 4 Joshua Tymon (Hull City), 6 Elliott Moore (Leicester City), 7 Japhet Tanganga (Tottenham Hotspur), 9 Demetri Mitchell (Manchester United), 10 Callum Slattery (Southampton), 12 Tariq Ukwakwe (Chelsea), 15 Daniel Kemp (West Ham United), 16 Luke Bolton (Manchester City), 17 George Hirst (Sheffield Wednesday, captain), 19 Martell Taylor-Crossdale (Chelsea)
Substitutions: 8 Harvey Barnes (Leicester City) for George Hirst 59, 2 Reece James (Chelsea) for Luke Bolton 66, 14 Elliot Embleton (Sunderland) for Tariq Ukwakwe 75, 18 David Brooks (Sheffield United) for Daniel Kemp 75
Substitutes not used: 1 Ryan Schofield (Huddersfield Town, goalkeeper), 3 Josh Grant (Chelsea), 5 Joseph Worrall (Nottingham Forest), 11 Ronaldo Vieira (Leeds United), 20 Ike Ugbo (Chelsea)
Head Coach: Neil Dewsnip
Goals: Hirst 25 (pen), Taylor-Crossdale 72 (pen)