The move means that the Japanese manufacturer will be able to continue to use its own software within the control ECU that will come into play in top-level grand prix racing in 2014.
An initial three-year agreement has been reached with series promoter Dorna to make the engines from the title-winning YZR-M1 available to teams that will operate in the CRT division of the championship.
This weekend's Qatar Grand Prix had been set as a deadline by Dorna for the conclusion of discussions between itself, the manufacturers and the FIM to ensure the continued support for the championship from its major competitors.
A statement issued "Yamaha Motor Co Ltd can confirm it has entered into an agreement with the MotoGP World Championship Promoter, Dorna Sports SL, to supply YZR-M1 engines on an annual lease basis to participating teams in the MotoGP Championship.
"The initial program will operate for the 2014-15-16 seasons.
"The agreement comes as a result of Yamaha's work with Dorna and the sport's governing body, the FIM, to further promote the MotoGP World Championship.
"The lease agreement facilitates an increase in competitive engines being available for teams competing in the premier class.
"The teams will then be free to develop their own bikes around the Yamaha engine or contract an independent chassis manufacturer to construct the complete bike."