The two-seater F-15 from the Japan Air Self-Defense Force crashed in waters off the central Ishikawa region during a training mission on January 31.
The body of the other pilot was recovered by the Japanese navy on Friday.
A naval search team recovered the second pilot's body on Sunday. The air force confirmed his identity, which was not released to the public.
The F-15 disappeared from radar soon after taking off from Komatsu air base for training.
The cause of the crash has not yet been established.
The defence ministry has not sought to ground Japan's F-15s in the wake of the incident.
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