Jones was stood down in March following a controversial radio interview in which he spoke about a report into the club's finances but stayed on as the CEO with protection under whistleblower laws.
In a statement issued soon after the team's 23-10 loss to Highlanders, the Brumbies announced the confidential deal which would see Jones leave after an "orderly handover" next week.
Settling the dispute quickly and outside of the courts would allow Brumbies to focus on rugby, said the side currently sixth in the Australasian Group on 20 points.
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"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," Brumbies chairman Robert Kennedy said.
"...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," he added.
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
