"The search and rescue operations are concluded," the air force said in a statement, adding that an analysis of recovered debris had "confirmed the death" of the 31-year-old pilot.
The air force said the aged jet had gone down 25 nautical miles (46 kilometres) south of Andravida military airport in western Greece during a daylight training flight.
The body of the plane's 29-year-old co-pilot had been found a few hours after the incident on Monday.
Greece's armed forces have declared a three-day period of mourning over the accident.
Almost to the day 27 years earlier, three Greek navy helicopter pilots died in a dramatic face-off with Turkish forces in the Aegean Sea on January 31, 1996.
The US-made F-4 Phantoms are among the oldest equipment in Greece's arsenal.
Greece acquired its first Phantoms in 1974 and last upgraded them about two decades ago.
The model originally dates from the 1960s.
According to the Panhellenic association of fallen aviators' families, another 18 airmen have died in F-4 Phantom accidents since 1977.
The last one was in 2004.
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