Hope Powell's side held off some intense pressure from the Japanese before going in front when Ellen White superbly lobbed in from 22 yards. They doubled their lead after the break when substitute Rachel Yankey took a touch and clipped in a smart finish.
In the last eight in Leverkusen at 1700 BST on Saturday England will play France, who lost 4-2 to hosts Germany.
The Germans topped Group A and go through to a quarter-final against Japan, who finished runners-up to England.
"We were very, very good today," said a delighted Powell. "You've got to respect Japan and the way they play, but we had a gameplan and we implemented it. They doubled their lead after the break when substitute Rachel Yankey took a touch and clipped in a smart finish.
In the last eight in Leverkusen at 1700 BST on Saturday England will play France, who lost 4-2 to hosts Germany.
The Germans topped Group A and go through to a quarter-final against Japan, who finished runners-up to England.
"We were very, very good today," said a delighted Powell. "You've got to respect Japan and the way they play, but we had a gameplan and we implemented it. They doubled their lead after the break when substitute Rachel Yankey took a touch and clipped in a smart finish.
In the last eight in Leverkusen at 1700 BST on Saturday England will play France, who lost 4-2 to hosts Germany.
The Germans topped Group A and go through to a quarter-final against Japan, who finished runners-up to England.
"We were very, very good today," said a delighted Powell. "You've got to respect Japan and the way they play, but we had a gameplan and we implemented it. The ambition was to get out of the group and top the group and we've done that. We're in the quarters and we'll have to do our best."
England should not fear either side after a display of endeavour and quality in Augsburg, marked by two goals of supremely clinical finishing either side of the interval.
Japan, who had beaten New Zealand and Mexico in their opening Group B games, impressed with their neat approach play and movement, but they could not find an end product to match.
England knew they could still qualify for the quarter-finals even if they lost the tie, with Mexico not only needing to beat New Zealand in the other game but having to improve their goal difference too.
The Mexicans took an early lead to put pressure on England and Japan threatened when Kozue Ando and Yuki Nagasato fired in shots which forced Karen Bardsley to save low down.
White had a shot deflected wide at the other end, but with 15 minutes gone England's nerves were calmed when White fastened on to a ball from the back and, with Ayumi Kaihori off her line, expertly lofted into the net.
The Japanese, who were already guaranteed a last-eight berth, continued to force England back, but Powell's rejigged defence - Sophie Bradley came in for rested captain Faye White - stood up to the task.
Striker White was a constant threat herself, seeing one wonderful hooked volley fabulously tipped over by Kaihori, but England made the game safe after 66 minutes.
Yankey, on as a half-time sub, took a touch to control Rachel Unitt's left-wing ball in and beat Kaihori with a classy dink over the keeper and into the net.
They played the rest of the game out in relative calm, while New Zealand produced a terrific fightback in Sinsheim, scoring twice in stoppage time to earn a 2-2 draw with Mexico.
In Tuesday's other match Nigeria beat Canada1-0 in Dresden, a third successive defeat for the Canadians.
England Ladies: Bardsley, Alex Scott, Unitt, Stoney, Bradley, Jill Scott, Clarke (Yankey 46), Asante, Ellen White (Bassett 90), Smith (Aluko 62), Carney.
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