The Samurai Blue beat Iran 3-0 in Monday's semi-final at the Hazza bin Zayed Stadium in Al Ain, with all of the goals coming in the second half.
Yuya Osako of Werder Bremen scored twice - one from the penalty spot - before Genki Haraguchi of Hannover 96 sealed the victory - and a place in the final against Qatar or hosts United Arab Emirates (UAE).
Muto was an unused substitute after returning from a one-match suspension for picking up two bookings in the competition.
The Newcastle man scored in a 2-1 victory against Uzbekistan in Japan's final group game, and has also featured in 1-0 wins over Oman and Saudi Arabia on Japan's route to the final.