The deal will open the door for player exchanges and sponsorship deals, as well as club friendlies and tournaments including both teams
The historic deal is the latest move in the J-League's expansion into South-Aast Asia; earlier this year the league sold broadcasting rights to Malaysia, Indonesia, Thailand, and Vietnam.
"As a team with an eye on expanding not just within Japan but around the world, we feel that by joining with a rapidly-developing Asian club we can help each other grow," Vissel president Koichi Kanaya said in a joint statement.
"Both of our clubs are eager to create new enterprises, and we're looking forward to being able to exchange ideas and information."
The deal will facilitate player and staff exchanges both at the professional and youth level, as well as friendly matches, the creation of new football schools, and marketing opportunities.
"We have for many years been strongly committed to 'development' at all levels of the club," wrote Chonburi FC chairman Wittaya Khunpluem in the announcement. "This is a new beginning for our club's history.
"We're incredibly happy to have partnered with a high-level club like Vissel Kobe, and I hope that we can use our relationship to raise the quality of our matches and personnel."