The team from Tokyo limited Waipahu, Hawaii, to four singles in a 4-1 win in the title game Sunday.
Japan won thanks to excellent pitching and defense, plus a homer and three RBIs from Konan Tomori.
The last international team to win the World Series was Curacao in 2004. The last time a team from Japan won was 2003.
Hawaii cut the lead to 2-1 in the fourth after a throwing error, but lefty reliever Ichiro Ogasawara got a strikeout and bouncer to end the threat. The 12-year-old Tomori added two insurance runs with his sixth-inning homer.
Starter Cody Maltezo allowed four hits and struck out four to lead Hawaii.