Yokohama beat Vissel Kobe 3-1 on Saturday to top the table on 68 points, two clear of Kawasaki Frontale, who beat FC Tokyo 3-2 despite playing with 10 for most of the game.
It is Yokohama's fifth title and their first since 2019, when former Socceroos boss and current Celtic mentor Ange Postecoglou triumphed.
Muscat's breakthrough follows a second-place finish in his first season in Japan, after joining the club in July 2021.
"I don't know (how I feel) at the moment, it's just a little bit surreal," Muscat told Japanese media.
"But just really proud. If there's an overriding emotion, it's pride - not only in the result, but the way we played, the way we won was tremendous and made me really proud.
"There's emotion, of course, and that's why the game is so great.
"For us, personally, we've been focusing on creating moments, many moments, through challenges ... and today, the moment that we created also created history.
"These guys will go down in history as one group that won the trophy for Marinos."
There were Australian flags among the Marinos supporters in the crowd and Muscat paid tribute to the fans.
"To see the support, not only today, but to see the unconditional support that we've had throughout the season - I hope you enjoy tonight, and party hard," he said.
The title race went down to the final day after Yokohama and Kawasaki both won in the penultimate round.
Elber's looping header in the 26th minute gave Yokohama the lead over Vissel Kobe, before Yoshinori Muto equalised just before halftime.
Takuma Nishimura restored Yokohama's lead in the 53rd minute, and 20 minutes later Teruhito Nakagawa tapped home to seal victory and the title.
Muscat has already signed a contract extension with Yokohama for next season but would surely be in contention to become the next Socceroos coach were Graham Arnold to move on after the World Cup.
The title completes Muscat's rebound from an ill-fated stint at the helm of Belgian top-flight outfit Sint-Truiden in 2020, where he was sacked after six months.
Muscat previously carved out a coaching legacy at Melbourne Victory, winning two A-League grand finals, a premiership and an FFA Cup before quitting in May 2019.
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