Manchester United striker Javier Hernandez's two second-half headers doomed Japan, who finished last in Group A as the only team without a point and a minus goal difference of five.
Alberto Zaccheroni's side also lost 3-0 to Brazil in the opening match and 4-3 against Italy on Wednesday. Brazil beat Italy 4-2 on Saturday to win the group and will face the runnerup of Group B in the semifinals.
Japan lamented their soft defense, which again leaked goals as fatigue set in during the second half.