World Rugby had cut its funding to the union in May pending a review into governance and administrative concerns which included "outstanding domestic legal matters" and the lack of properly audited financial settlements.
A new committee will oversee a roadmap for the operating structure of the union until the end of 2024.
"The Tonga Rugby Union's challenges are well documented and we have been working with all parties to identify and agree a roadmap to return Tonga to where it deserves to be, on and off the field," World Rugby chairman Bill Beaumont said in a statement.
"Through this tripartite agreement, the conditions, expectations and framework has been set to do just that and I would like to thank the Tongan government for their understanding and support."
All three parties agreed to recruit a new CEO who would be selected and approved by representatives of the joint management committee, which also has representation from Pacific Rugby Players (PRP).
"We have worked hard for many months alongside World Rugby, TRU and the Tongan government to keep players interests at the forefront while we find solutions," PRP chairman Hale T-Pole said.
"PRP being part of the joint management committee going forward is a significant step for the players and we will play our part in shaping a positive next chapter for Tonga rugby."