The move ensures that a single Great Britain team will continue beyond the 2012 Olympics as part of a revamped set-up that is likely to bring the British Basketball League and a new women's league under a single umbrella.
FIBA has backed the merger despite a decision by Wales to reject the chance to join the new body. However, the plan will now go forward to UK Sport for approval.
"We still have to get some clarity on how the new body will be recognised because of the Welsh decision," said Kevin Pringle, Basketball Scotland chief executive. "But we all took our decisions independently. FIBA have said they're comfortable with us and England coming together."
Under the agreement, Scotland would stop competing independently in official competitions from 2016 onwards although an exemption has been granted to field national teams at under-16 level until 2020. The home nations would also enter their own sides at the 2018 Commonwealth Games in Queensland.
"[The] decision will accelerate the development of the sport in Scotland," said Patrick Baumann, Secretary General of FIBA.