Liverpool midfielder Endo started and finished the last-16 tie in Doha, which was won by goals from Ritsu Doan, Takefusa Kubo and Ayase Ueda.
Doan put Japan ahead on the half-hour mark and Kubo doubled their advantage in the early stages of the second half.
Bahrain then pulled one back thanks to a Zion Suzuki own goal, but Ueda struck in the 72nd minute to seal the Samurai Blue’s place in the last eight, where they will face either Iran or Syria on Saturday.
