Goals from Takuma Asano and Yosuke Ideguchi gave the home side a deserved win that guaranteed their place at next year's finals in Russia.
The Socceroos struggled throughout to threaten the Japan goal and have now failed to win in five outings since their 3-2 victory over Saudi Arabia in June.
The result leaves them in third place in Group B, behind Bert van Marwijk's side on goal difference, meaning they must beat Thailand on the final day and hope Japan can avoid defeat in Jeddah if they are to seal the second automatic qualifying spot.
Postecoglou took responsibility for the result and was frustrated that his side could not make the most of the possession they had.
"The team we put out there was certainly good enough to get the job done," he told Fox Sports.
"I'll take responsibility for team selection and the way we played. Tonight's result is on me, not the players or the ones who are missing.
"We didn't have the night we wanted to. It's a bit hard to sum it up right now because obviously we're disappointed with the outcome.
"We had our moments but we just never really got control of the game, particularly our midfield. We had some possession but we didn't really threaten as much as we could have.
"The first goal really killed us. [We are] obviously disappointed."
Postecoglou hopes home advantage makes a difference when they take on Thailand in Melbourne on Tuesday.
"We've got to play well first. Being at home will make a difference. We've got to win. Unfortunately, we've got to rely on another result," he said.
"We'll see what happens. We'll do our job and see what happens."