The search for Capt. Nicholas Giglio, who has been missing since Thursday night's crash, was shifted to a recovery effort looking for his body and the plane's wreckage.
Investigators believe the bottom of the other jet struck the top of Giglio's fighter and pierced the pilot's canopy, Air Force Col. Joe Guastella said. The other pilot was not injured and was able to land his plane safely.
Investigators came to their conclusion using data gathered from the second plane and an interview with the other pilot. Also, radio beacons on the aircraft and the pilot were never activated, indicating Giglio never left the cockpit, Guastella said.
"He had no opportunity to eject from the aircraft," Guastella said.
The Coast Guard, which spent nearly two days looking for the pilot in 8,000 square miles of ocean about 40 miles northeast of Charleston, has now shifted to trying to recover the jet, said Capt. Michael McAllister, director for the search.
The collision happened as Giglio and the second pilot, Capt. Lee Bryant, were in a night training exercise. The pilots had finished most of their maneuvers and were getting ready to head home when they hit, Guastella said.
The flight controls of Bryant's jet were miraculously not damaged, and he managed to land at Charleston Air Force Base without injury, Guastella said.
The two pilots were part of Shaw Air Force Base's 20th Fighter Wing commanded by Guastella. Giglio, originally from New Jersey, has been a fighter pilot for 18 months and is part of the 77th Fighter Squadron that is training for deployment to Iraq early next year. He took his first F-16 flight with Guastella, who was an instructor then.
"He is a patriot and a great American," said Guastella, who told Giglio's family about the investigators' findings a few hours before the public announcement.
Giglio, 32, leaves behind a wife, a young daughter and a baby on the way, Guastella said.
The 20th Fighter Wing hasn't flown since the collision and will likely remain grounded until Tuesday, its commander said.
Officials said after the crash that there were reports of debris and an oil slick in the water, but investigators haven't determined if that came from Giglio's jet. The water is about 50 feet deep in the area where the Air Force thinks the F-16 went down, McAllister said.
The Coast Guard used its helicopters and boats as well as private volunteers who helped in the search.
"If Capt. Giglio had ejected safely from the aircraft, we're confident we would have found him," McAllister said.
Associated Press Writer Bruce Smith in Charleston contributed to this report.