Takefusa Kubo had signed for the Spanish giants in 2011 to train at their famed La Masia academy but the club were found guilty of "serious" youth transfer breaches between 2009 and 2013 by world governing body FIFA last year.
Barcelona were handed a 14-month transfer ban, which was briefly lifted when they launched an unsuccessful appeal, meaning they are unable to recruit any new players until the 2016 January window.
The teenager, the first Japanese to sign for Barcelona, was forced to leave the Champions League finalists and had been training in his homeland since April, Kyodo News reported, before opting to sign with the J.League title challengers.
"We hope in the future, he becomes a player who can carry the Japan national team or the Olympic team," Tokyo club president Naoki Ogane was quoted as saying.
Kubo could rejoin Barcelona when he turns 18.
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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