The Guardian Unlimited website reports that the agreement ended a drama that began in September when players went on strike for the first time in the game's 70-year history in Japan in protest at a planned team merger.
The labour action won overwhelming support from the fans and prompted the teams' management to agree to allow the entry of a new club.
The new team - the Tohoku Rakuten Golden Eagles - will play in the north-eastern city of Sendai from next season.
Rakuten edged out Internet services firm Livedoor Co. which had also been vying to establish a team in Sendai.
The entry of Rakuten and Mikitani to Japanese baseball ownership is a watershed for the sport, whose owners have traditionally been from the railroad, food service and media industries.
