Ellen White put England ahead after 15 minutes at SGL Arena when she latched onto a pass from Karen Carney to lob the ball over Japan goalkeeper Ayumi Kaihori.
They had to wait until the 66th score their second, with substitute Rachel Yankey controlling a cross from Rachel Unitt before putting the ball past Kaihori to secure a win.
The result helped England leapfrog Japan into first place in Group B, with England now meeting France in Leverkusen on Saturday in a quarter-final.
Group B's other match was a thriller, as New Zealand scored two goals in injury time to salvage a draw against Mexico. England's win over Japan, however, meant pride was the only thing at stake.
Goals from Stephany Mayor and Maribel Dominguez gave Mexico a 2-0 lead inside the opening half-hour, but New Zealand hit back in the first minute of stoppage time through Rebecca Smith and Hannah Wilkinson scored another in the 93rd minute to ensure a point.
In Group A, Germany's 4-2 win over France in Moenchengladbach saw them claim top spot, setting up a quarter-final showdown with Japan on Saturday.
Kerstin Garefrekes put the host nation ahead after 25 minutes and when Inka Grings scored on 32 minutes Germany looked to be in cruise control.
Marie Delie pulled a goal back for France 11 minutes after half-time, but Grings restored a two-goal buffer with her second in the 68th minute.
Laura Georges made it 3-2 four minutes later but Germany finally killed the game off with an 89th-minute goal to Celia Okoyino da Mbabi.
Also
in Group A, Nigeria made sure they did not finish bottom when a late
goal from Perpetua Nkwocha handed them a 1-0 win over Canada, who go
home pointless from their three matches.
Wednesday 6 July
Time | ||
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09:20 | Adelaide secure Socceroo | |
07:46 | Colombia boss: ´How do I mark Messi?´ | |
03:14 | Gasperini happy with Inter talent |