The board dropped a bombshell on players, coaches and fans when they announced they had been able to reach a settlement with Jones after more than a month of court-room battles and behind-the-scenes power struggles.

Both parties have declared they will not comment any further after a debacle that engulfed the whole organisation.

But questions will remain about the Brumbies' financial stability after legal fees and a significant payout, believed to be more than $700,000, as well as a fight to try to win back fans.

Former Brumbies star Joe Roff has been floated as a potential candidate for months, and the Brumbies board will start an immediate search for Mr Jones' replacement.

However, there is speculation that the Brumbies could split the chief executive role in two with Roff as a leader of the rugby department and another person taking control of the business operations.

The Brumbies players and coaching staff were left stunned at the announcement, which happened with less than 10 minutes to go in their 23-10 loss to the Otago Highlanders in Invercargill.

Jones had been fighting to save his position as chief executive after the board stood him down on March 21. He was successful in gaining an injunction for whistleblower protection.

It remains unclear whether the ACT Supreme Court case against the Brumbies board, University of Canberra, its vice chancellor Stephen Parker, Joe Roff, David Lamont and the University of Canberra Union will go ahead.

However, it could prompt the easing of a suppression order on a KPMG report into Brumbies transactions from the sale of their Griffith headquarters and move to the University of Canberra.

Brumbies fans have been left jilted by the stoush that led to a divide in Canberra's club rugby community and filtered into the playing ranks when Scott Fardy and Stephen Moore were named in a report on Friday alleging a potential workplace investigation.

Jones was determined to fight for his role and declared two weeks ago that he wanted to be the Brumbies' long-term chief executive.

But the infighting and battle took its toll, with Jones agreeing to walk away.

Brumbies chairman Robert Kennedy released a statement as the Brumbies were trailing the Highlanders, saying that there would be an "orderly handover" of Jones' job this week.

"I want to reassure our business partners, stakeholders, players, staff and members that the board has full confidence in the remaining executive management team within the Brumbies and our current financial position to continue operations throughout the 2016 season," Kennedy said.

"We are immensely proud of our rugby program at the Brumbies and once again we've had a positive start to the season both in terms of on-field results and crowd support. I would ask all Brumbies fans to rally behind the team and continue to show their support in what we hope will be another successful year."

Kennedy must now try to find a new chief executive in uncertain times as the ARU attempts to restructure Australian Super Rugby to operate under one management system.

He must now also face questions about the club's future as fans scrutinise the process of the fallout and seek answers for a saga that ripped apart the Brumbies.

The Brumbies confirmed on Saturday night there was no workplace investigation into Moore and Fardy's conduct.

"The board and management take the issue of workplace behaviour very seriously and ensure that any complaints received are dealt with appropriately to ensure the rights of our players and staff are protected," a board spokesman said.

The Brumbies have now won just two of the past six games, coinciding with the off-field drama that led to Jones leaving his post.

The terms of the handover will remain confidential, but if the Brumbies committed to a significant payout of Jones' contract it could have massive financial ramifications for the organisations.

The Brumbies lost $1.68 million last year and the proceeds of their $11.375 million sale of Griffith have almost disappeared.

The board released a statement saying: "Both parties believed that it was in the best interests of the Brumbies that this dispute be settled quickly and outside of the courts so that the focus can return to the players and the team and the great club of the Brumbies."