The Samurai Blue, who had already been assured of a place in the knockout phase having won their first two matches, will now take on Egypt in Manchester for a place in the last four, while Los Catrachos meet Brazil in Newcastle.
The first 35 minutes were heavy on fierce tackles and shy on goalmouth action. Yuki Otsu had Japan’s best chance, but his shot from distance went straight at goalkeeper Jose Mendoza, while Antony Lozano fired well wide from 35 metres following a neat dribble.
The finest opportunity of the first half came with six minutes remaining. Johnny Leveron dinked a delightful ball over the top for Jerry Bengtson, who jumped and, with his chest, brilliantly pushed it past two opponents and into his stride. The Honduras No11 unleashed a low shot, but Shuichi Gonda flung himself south-east to repel the effort, before bravely diving on the loose ball as Mario Martinez loomed.
Japan began the second half in the asendancy, yet they failed to come close to breaking the deadlock until the 81st minute, when a mishit Takashi Usami free-kick almost dipped under the crossbar, only for Jose Mendoza to punch it over.
The Honduras keeper then made an excellent save to deny substitute Kensuke Nagai from close range, before making a fine catch from a powerful Kazuya Yamamura header in the last minute.
The result left Japan on seven points and Honduras on five, three clear of third-placed Morocco.