Football Federation Australia had been under threat of a takeover by FIFA after failing to pass requested reforms at its annual general meeting last week.
It had been set a November 30 deadline to expand its membership and create a more representative congress, with the world body threatening to establish a committee to run the game in Australia if it failed to do so.
But after a resolution to pass the proposed reforms fell short of the 75 percent voting threshold, FIFA has opted for a softer approach.
It will instead send a team to oversee and mediate a final round of talks along with officials from the Asian Football Confederation in Sydney early next year.
"FIFA's ruling gives all of us a chance to take a fresh look at how the congress can best represent the Australian football community, with the direct involvement of FIFA and AFC officials in that process," FFA chairman Stephen Lowy said in a statement.
"In a wider sense, this process will enable all Australian stakeholders to work together on a shared vision for our game at every level."
Lowy has had a rocky relationship with the Australian Professional Football Clubs Association -- the lobby group formed by the A-League's 10 clubs -- which claims he has "lost the dressing room".