Goalkeeper Yushi Sekiguchi saved three penalties in the shootout as Japan claimed the title following a 2-2 draw after extra-time.
Japan twice came from behind through Kotaro Inaba and an extra-time own goal from Hamid Ahmadi after Farhad Tavakoli and Hossein Tayebi had given defending champion Iran the lead.
And in the shootout, Sekiguchi saved from Mohammad Taheri, Ghodrat Bahadori and Asghar Hassanzadeh, with Kazuhiro Nibuya, Tomoki Yoshikawa and Akira Minamoto converting for Japan to seal a 3-0 victory.
Sixteen teams will be vying for the AFC Futsal Asian Cup Thailand 2024 title when the 17th edition kicks off in Bangkok on April 17.
Japan is the defending champion while Iran will be seeking a 13th title with the teams the only sides to have emerged champions in the history of the tournament.