Bernie Ecclestone's Formula One Group has agreements in place with 10 of the 11 teams about the new commercial terms, with Marussia the odd one out. Meanwhile, Todt has been pushing for FIA to receive a greater share of F1's profits.
"I am very pleased that the agreement ... has been concluded," Ecclestone said.
One of the noteworthy aspects of the agreement is a new tender procedure for appointing single suppliers for tires and fuel in F1.
In the new process, the FIA will conduct the tender process and the commercial rights holder is entitled to run negotiations with potential suppliers, with a view to the selected supplier being officially appointed by the World Motor Sport Council.
Following the WMSC meeting in Croatia, members also accepted Todt's proposal for a new task force looking at ways to allocate additional financial resources for the FIA and its members. This would only come into place after the December elections.
Todt and Ecclestone have also had to contend with other issues.
Todt is hoping to be elected for a second term as president in December when he goes up against challenger David Ward. Ecclestone has been charged by German prosecutors with bribery over a $44 million payment, placing his future in doubt.
The 82-year-old British billionaire has been under investigation since a German banker was convicted of receiving the payment from Ecclestone in connection with the sale of a stake in F1. A German court decision on whether to try him has been delayed until next year.