Rugby Australia assumed ownership of the Brumbies on Tuesday, as the governing body's push for greater control of the domestic game gained momentum.
Faced with a precarious financial position and a decline in their international standing, Rugby Australia has been looking to take control of the country's four Super Rugby teams.
Centralisation would allow Rugby Australia to pool stretched resources with the aim of improving performance – a model similar to New Zealand and Ireland.
The Brumbies have followed Waratahs in ceding control to Rugby Australia, but the other Super Rugby sides, Reds and Western Force, have so far resisted.
"Through taking on the Brumbies business, Rugby Australia has committed to managing and supporting the organisation through an exciting period for rugby in Australia," Brumbies chief executive Phil Thomson said in a statement.
Rugby Australia said it would take ownership of the Brumbies' "professional rugby operations and related business assets".
Brumbies are one of Australia's most successful sides and were the only non-New Zealand team to make the semifinals in Super Rugby this year.
The debt-laden Melbourne Rebels were shut down by Rugby Australia at the end of the Super Rugby season last month.
A long-time powerhouse of international rugby union, two-time World Cup winners Australia are currently eighth in the world rankings.
Last year the Wallabies failed to make the World Cup quarterfinals for the first time in their history under Eddie Jones.
New coach Joe Schmidt enjoyed a winning start when Australia beat Wales 25-16 on Saturday.