The ARU has committed to cull either the Rebels or the Perth-based Western Force as part of a revamp of the competition for next season.
The Force entered into arbitration with the governing body last week and if the mediation comes out in favour of the Western Australian side, the ARU's options will be limited.
One option would have been to buy out Rebels owner Imperium Sports Management (ISM) and close down the team, but the transfer of ownership to the VRU would appear to have stymied that potential move.
Certainly, ISM managing director Andrew Cox believed the transfer had removed the axe hanging over the head of the franchise.
"Its exciting for the Melbourne Rebels and local rugby that, with the VRU, we've been able to secure the future of the Super Rugby club," he said.
An ARU statement on Saturday made it clear that the governing body had not been informed of the transfer of ownership and indicated they would need to approve it.
A statement from the VRU on Sunday, however, said they had held an ARU-approved "put option" - an agreement which allows but does not oblige a party to purchase shares for a fixed price by a future date - in place since June 2015.
"Today's announcement sets in place the foundations for a secure and positive future for the Melbourne Rebels and Victorian Rugby," the statement concluded.
Local media reported over the weekend that ISM, who took control of the team in 2015, had sold the shares for A$1.
Southern hemisphere rugby's governing body SANZAAR agreed earlier this year to reduce Super Rugby to 15 teams from next season against a backdrop of falling revenues and fan interest after the expansion to 18 sides last year.
Two South African sides, the Cheetahs and Southern Kings, have already departed and will join Europe's Pro-12 league, expanding that competition involving clubs from Ireland, Scotland, Wales and Italy to 14 teams.
(Reporting by Greg Stutchbury in Wellington; Editing by Peter Rutherford)
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