City, owned by Abu Dhabi's Sheikh Mansour, have already bought Australian club Melbourne Heart and are launching the New York City Football Club next season as part of their commercial expansion from their base in northern England.
"We're thrilled to be able to play a role in investing and building on the ongoing success of YF Marinos," City chief executive Ferran Soriano said in a statement on Tuesday.
City are taking a stake of less than 20 percent in the Japanese club, which has long established ties with the Nissan car company who remain its main backer.
The Premier League club will provide support in areas like training methods, coaching and medical care to YF Marinos who have not won the J-League since 2004. In return City will get additional revenues and a chance to boost their brand in Japan.
The deal was described as the first significant foreign investment in a Japanese J-League team.
"The YF Marinos is an excellent soccer club with a rich history which has grown hand in hand with Nissan," said Carlos Ghosn, Nissan President and CEO.
"This partnership will contribute to the growth of the club, the club's hometown and Japanese soccer," he added.
City, English champions twice in the past three seasons, have been fined and had their Champions League squad size capped for next season after falling foul of Financial Fair Play rules.
The club say that they are on course to move into profit from next season after Sheikh Mansour ploughed hundreds of millions of pounds into creating a team capable of competing with the best in Europe.
(Writing by Keith Weir, 44 20 7542 8022; editing by Martyn Herman)
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