The A-League will become a self-governing body in 2021 after protracted negotiations resulted in the "unbundling" of the top flight of professional soccer from Football Australia.
Football Australia made the announcement on Thursday and the new structures will be put in place throughout the remainder of the 2020/21 season.
The A-League and women's W-League will now be governed by the Australian Professional Leagues (APL) and hope to use their new operational and commercial independence to generate greater revenue.
"This is an historic moment for the future of football in Australia -- for the fan, for the player, for the whole game," Western Sydney Wanderers co-owner Paul Lederer, who will chair the APL board said in a statement.
"The handbrake on the game is off. Owners can finally invest in what they own and create value for the entire footballing ecosystem."
Greg O'Rourke, who has been running the A and W-Leagues since 2016, has been appointed APL commissioner but the body will continue to work closely with Football Australia, which changed its name from Football Federation Australia last month.
"We have been able to create a unique model which draws upon global best practice whilst allowing for local specificities," Football Australia chief executive James Johnson said.
"Significantly, the model establishes a framework for a strong partnership between Football Australia and the APL which recognises the value of a thriving domestic professional league to the ongoing growth of the game in Australia."
The battle for control of the professional game between the A-League clubs and Football Australia has been running for several years.
In 2017, a joint delegation from global governing body FIFA and the Asian Football Confederation travelled to Australia to try and break an impasse between the two parties.
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