Marinos lifted the trophy after a 3-1 win away to Vissel Kobe on the final day, clinching the title two points ahead of defending champions Kawasaki Frontale, who beat FC Tokyo 3-2.
Muscat follows in the footsteps of current Celtic manager and Australian compatriot Ange Postecoglou, who led Marinos to the title in 2019.
“At the moment it’s just a little bit surreal,” said former midfield hard-man Muscat, who joined Marinos in summer 2021 when Postecoglou left to take over at Celtic Park.
“I’m just really proud, I think if there’s an overriding emotion it’s pride. Not just the result today but the way we played made me really proud.”
Marinos squandered several chances to wrap up the title over the final weeks of the season and saw their eight-point lead reduced to just two as Kawasaki kept up the pressure.
Marinos took the lead against Kobe through Elber but the home side, who started with former Barcelona legend Andres Iniesta on the bench, equalised in first-half injury time.
Takuma Nishimura edged Marinos back in front in the 53rd minute before Teruhito Nakagawa added another for insurance 20 minutes later.
Kawasaki took an early lead against Tokyo but then had goalkeeper Jung Sung-ryong sent off for a wild challenge in the 29th minute.
Kawasaki, who had won the title in four of the previous five seasons, went on to claim the win but it was not enough to catch Marinos.
“There’s emotion, of course, and that’s why the game is so great,” said Muscat, who managed Melbourne Victory to two A-League titles in his native Australia.
“We’ve been focusing on creating moments, and today the moment we created also created history. These guys will go down in history as one group that won the trophy for Marinos.”