"We will continue to do everything we can to assist our families and airmen at this tragic time."
The US air force recently returned to service nearly all of its F-15 A to D jets, after grounding them following the crash of an F-15C in Missouri in November 2007.
The pilot in that case ejected safely and emerged with minor injuries.
About 450 aircraft, about 60 per cent of the air force's F-15 fleet, were grounded for inspections following that crash, but only nine F-15 A to D jets remain grounded, an air force spokeswoman said.
James Harless, a coast guard petty officer, said that a rescue jet located one of the pilots and communicated the location to a fishing vessel, which picked him up and then passed him on to a helicopter.
Rescuers were told by the pilot that he saw the second pilot eject, but lost him in the clouds, Harless said.
With his approximate location determined, the second pilot was found by a coast guard helicopter.
Both men were then taken to the Eglin base hospital.
The weather in the area at the time of the incident was reportedly calm, but an investigation into what caused the collision will be carried out, officials said