Captain Michael Johnston, 57, was piloting the Airbus A320 plane with 147 passengers and five crew members when he became gravely ill and later died. The co-pilot then took control of the plane and landed the jet safely.
Crew members "took extraordinary care of Mike, each other and our customers," American Airlines CEO Doug Parker said in a statement sent to employees.
"We couldn't be more proud of the teamwork this crew showed during an extremely difficult time."
An autopsy and preliminary toxicology tests "showed that the death was the result of natural diseases," the Onondaga County, New York, medical examiner's office said -- without offering specifics.
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Johnston's wife had a double bypass surgery in 2006. She said she was told he likely died of a heart attack, CNN reported.
"Medical emergency, captain is incapacitated," someone in the cockpit told an air traffic controller, according to audio posted to LiveATC.Net. "Request handling for runway."
Passengers expressed sadness about what happened and gratitude they arrived safely.
"If it wasn't for the copilot using a cool head," passenger Peter McSwiggin said, "it might have been more disastrous."
Aviation experts said there was never any danger to passengers because pilots and co-pilots are equally capable of flying.
Captains and co-pilots usually take turns flying and doing takeoffs and landings, said former airline pilot James Record, who teaches aviation at Dowling College in New York was quoted as saying.