The Agreement is F1's tri-partite pact that governs the commercial arrangement between the FIA, the teams and the sport's commercial rights holders, CVC Capital Partners.
The sport has been operating this season without a Concorde since the previous deal expired at the end of last year.
In July, over the course of the Hungarian Grand Prix weekend, F1 supremo Bernie Ecclestone and FIA president Jean Todt set out the framework for implementation of the new Agreement that runs through to 2020.
A statement released by the FIA has confirmed that framework "has now come into force following the approval of the respective governing bodies of the signatory parties".
The statement added: "This agreement provides the FIA with significantly improved financial means to pursue its regulatory missions and to reflect the enhanced role undertaken by the FIA motor sport.
"The parties have agreed a strong and stable sporting governance framework which includes the Formula One Group, the FIA and the participating teams.
"The agreement lays down solid foundations for the further development of the FIA Formula One World Championship.
"Now that the agreement is operative, the parties will move towards the conclusion of a multi-party Concorde Agreement."
The final point refers to the fact all 11 teams now need to be on board as Ecclestone previously negotiated bi-lateral agreements with 10 of the marques, with the exception of Marussia who remain in talks.
Todt said: "We can be proud of this agreement, which establishes a more effective framework for the governance of the FIA Formula One World Championship.
"The FIA looks forward to continuing to fulfil its historic role as the guarantor of both regulation and safety in F1 for many years to come."
Ecclestone added: "I am very pleased that the agreement between the FIA and the Formula One Group has been concluded".