It was a crushing blow for an understrength Socceroos who now face a perilous play-off to keep alive their hopes of making Qatar.
The game in a wet Sydney looked destined for a draw before Mitoma converted from close range on 89 minutes, and then again after a mazy run in injury time to spark joyous celebrations from the visitors.
Australia now cannot finish higher than third, forcing a play-off against the third-placed team in Asian Group A. The winner will then meet a team from South America for the right to play in Qatar later this year. Australia were also missing a string of players due to coronavirus impacts or injury, including influential duo Aaron Mooy and Tom Rogic.
"But at the end of the day we've got the third-place spot and you've got to be positive about that. We've just got to move forward. I've always said I believe in these boys and it's one game at a time."An energetic Japan started strongly with Liverpool star Takumi Minamino testing Socceroos keeper Mat Ryan inside the first minute.
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