The club was wound up by the ATO in August, after it had already been stripped of its A-Leagues licence, then vowed to fight that decision.
Facing liquidation, United's ownership West Melbourne Group had an interlocutory hearing in the Federal Court on Thursday morning.
Justice Penelope Neskovcin ordered the parties into mediation, indicating that was the "last shot" for a resolution.
After several hours, the parties returned with an agreement in the afternoon. Provided payment is completed by January 7 orders to wind up WMG Football Club (United) will be set aside.
Major lender Johnson Controls is set to pay the required $15.5 million to cover the ATO debts.
In the morning's hearing, it was also noted Lederer Group Pty Ltd had proposed to step in further funding.
The founder of Lederer Group is billionaire Paul Lederer, the former Western Sydney Wanderers chairman.
Mr Lederer is still a shareholder and club director at the Wanderers but stepped down as chairman last June.
The road ahead remains unclear for United, who remain a club in name only - with no players and few staff on the books as they sit out the ongoing season.
Facing a tax bill amid concerns over unpaid wages and superannuation - and while under a FIFA registration ban - Western were stripped of their A-Leagues licence by Football Australia (FA) in August.
The wind-up order followed, and men's and women's players and staff were all left in limbo before the Australian Professional Leagues put the club into hibernation before the current seasons.
The club welcomed Thursday's development as it maintains ambitions to return to Australian soccer's top flight.
"Today's outcome is a positive step forward for Western United Football Club," the club said in a statement provided to AAP.
"It provides a clear pathway for the club to reset as we move into the next phase of our future and our eventual return to the A-Leagues.
"We are deeply appreciative of the patience and resilience shown by our members, partners and staff throughout this difficult process, as well as the support of Wyndham City Council and Stephen Conroy and the APL.
"Further details on the direction of the club and the broader project as well as additional comment will be shared in due course."
