The pilot of the other jet ejected and suffered minor injuries.
The two aircraft collided Wednesday during a combat maneuver in the Vosges region near the town of Colombey-les-Belles, the defense ministry said in a statement late in the day, AP reported.
The pilots who were killed were an instructor and a trainee on a training mission, it said.
Military and judicial investigations are underway into the causes of the accident.
The pilot of one Rafale was found alive soon after the crash, but it took several hours of searching by gendarmes in the wooded region to find the two pilots of the other jet.