Japan will be the first Asian team in the Super Rugby competition when the championship expands for the 2016 season.
Its competing bid from Singapore has effectively conceded defeat.
It leaves the way open for the Japan Rugby Football Union, which will host the World Cup in 2019, to put together Asia's first team in the championship.
The governing body SANZAR said all that is needed now is a formal participation agreement with Japan.
The new format of the competition will feature two South African conferences, one of which will include the Asian team.
It coincides with the renegotiation of the broadcasting agreements that financially underpin it.