Tries from Kotaro Matsushima, Yoshikazu Fujita and Amanaki Mafi helped earn a another well-deserved victory, but the occasion in Gloucester was the ultimate anti-climax, coming three weeks after they shocked the tournament by beating South Africa.
Despite falling to their fourth defeat, the U.S. were no pushovers and ended their own campaign with a spirited performance as tries from Takudzwa Ngwenya and Chris Wyles kept them in the contest throughout.
Scotland's victory over Samoa on Saturday had ensured that Japan, who will host the tournament in 2019, could finish no better than third in Pool B, and they ended two points adrift of the Scots and four behind group winners South Africa.
"It's disappointing but we had a great World Cup. We played as well as we can today," Japan coach Eddie Jones said.
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"It has been fantastic. The guys have all played above themselves and worked hard and with a real spirit and how rugby should be played."
Following the advent of five-team groups in 2003, no team had won three of their four pool stage encounters and not progressed to the next round.
Yet Japan's failure to pick up bonus points in any of their matches and their tired defeat to Scotland four days after their Springbok shock proved to be their undoing and ensured there was nothing but pride to play for at the Kingsholm Stadium.
That and another opportunity to show-off their well-honed technical skills and remind everyone how far they have progressed having won only one game in all their previous World Cup campaigns.
After AJ MacGinty landed an early penalty for the U.S., Japan responded with their first foray into American territory, switching the ball from one flank to other with swift hands to leave Matsushima free to cross in the corner.
The U.S. hit back with Ngwenya touching down, after a raking pass from Wyles, for his first World Cup try in eight years.
The Japanese again took swift retribution, however, as Yoshikazu Fujita sneaked through a heaving mass of bodies to score and an Ayumu Goromaru penalty gave the Japanese a comfortable 17-8 lead at the break.
The sides exchanged penalties at the start of the second half, but a yellow card for U.S. prop Eric Fry proved a debilitating blow as Japan extended their advantage within a minute with Mafi driving over the line from close range for a third try.
The U.S. did not lie down and MacGinty launched a superb long pass out to the right flank for fullback Chris Wyles to touch down.
MacGinty's conversion briefly reduced the deficit to seven points before another Goromaru penalty rounded off the scoring.
The Gloucester fans gave Japan a rousing send-off and they can now build for their 2019 tournament with the sport on a high in their own country.
(Writing by Toby Davis; editing by Mitch Phillips)
