Eintracht, currently 12th in the Bundesliga after two games, said in a statement they had agreed to the 27-year-old's request to cut short his contract which runs until June 2016.
"I've had three wonderful seasons here. My time at Eintracht will always remain a wonderful memory," said Inui.
Inui arrived in Germany in 2011 from J League side Cerezo Osaka, playing first with Bochum before joining Frankfurt the following season.
He played 75 matches with the club, scoring seven goals.