It was the first time the World Cup 2022 hosts had lifted the trophy and means Muto had to settle for bringing a runners-up medal back to Tyneside.
The Newcastle forward - who has scored once in the competition - started on the bench at the Zayed Sports City Stadium in Abu Dhabi.
And by the time he entered the fray in the 62nd minute, his team were 2-0 down to goals from Almoez Ali and Abdulaziz Hatem.
Japan - who were chasing their fifth Asian Cup title - pulled one back through Takumi Minamino, but Akram Afif converted from the spot after Southampton's Maya Yoshida had handled in the area to seal the victory for Qatar.
Muto will now return to Newcastle and is expected to rejoin his Magpies team-mates next week, ahead of their Premier League trip to Wolverhampton Wanderers.