Japan broke the spirit of Paul Okon's side, scoring two goals, including a penalty, in first half stoppage time.
Koki Ogawa added a third after 71 minutes to ensure Japan topped its group with a perfect record from its three games.
The Young Socceroos, who finished on six points and a goal difference of plus-five (+5) from its three games, progressed to the finals as one of the five best second-placed teams - joining the 10 group winners and host nation Bahrain.