Japan finished top of the group with seven points from three games and they will take on Egypt in the last eight.
Runners-up Honduras will face a more daunting test against one of the tournament favourites in Brazil.
Honduras showed more enterprise and created the best two chances of a low-key opening 45 minutes, but Japan showed more urgency in the second half.
But both sides struggled to carve out clearcut opportunities although the goalkeepers were pressed into service at both ends.
