Nearly 100 of Australia's best referees had been on strike since September 4.
FA had proposed a structure whereby referees would be contracted not to the sport's national governing body but directly to the Australian Professional Leagues (APL).
On Friday, FA announced a shared framework had been reached with the Professional Football Referees Australia (PFRA) for the 2026-2027 season, with discussions to continue regarding a longer-term agreement.
Referees will be contracted and employed by FA, with the APL covering the costs for their matches.
"Referees are highly valued members of our game, and we are pleased that Football Australia, the APL and PFRA have come together around a shared path forward for Australian refereeing," FA chief executive Martin Kugeler said in a statement.
"The dialogue over recent weeks has been constructive and respectful.
"Each party has approached the discussions with a genuine commitment to strengthening refereeing and ensuring the interests of the game remain at the centre of our thinking.
"Referees will be contracted and employed by Football Australia with the APL covering the costs for A-League matches.
"This provides a strong platform for the 2026/27 season, while giving all three parties the opportunity to continue working together on how we further strengthen and develop refereeing in Australia over the longer term.
"We have an outstanding group of Australian referees, and we now look forward to seeing them on the pitch as our attention turns to an exciting period of football ahead."
PFRA president Evgeny Vizelman welcomed the resolution as providing referees with certainty while pushing for further professionalism.
"The PFRA welcomes the agreement reached with Football Australia, which provides our members with the immediate certainty they need and allows our referees to return their full focus to officiating," Vizelman said in a statement.
"Importantly, this agreement also creates an opportunity for ongoing collaboration regarding the longer-term future of elite refereeing.
"We remain committed to working constructively with Football Australia and the APL to develop a sustainable structure that supports the continued growth and professionalisation of refereeing in Australia.
"We believe there is a genuine opportunity to build something that works for all parts of the game.
"Our members are looking forward to getting back on the field and to working with both organisations to ensure Australian refereeing continues to progress domestically and on the international stage."
APL chief executive Steve Rosich had been adamant the dispute would be resolved in time for the season-opening Sydney derby on October 16 at Allianz Stadium.
"We have liaised closely with Football Australia on this, and we're pleased a resolution has been reached," Rosich said.
