Lifeguard Lt. John Everhart says someone walking on the beach discovered the body before dawn Thursday at Tourmaline Surf Park.
Everhart says the body had wounds consistent with a shark attack. The medical examiner concluded the attack occurred after the surfer had died.
The man has been identified as a 42-year-old San Diego resident. He was surfing the night before when lifeguards lost sight of him a half-mile north of Crystal Pier.
Late Wednesday lifeguards found a surfboard and wetsuit about 300 yards off the beach where the surfer was first seen.
The Coast Guard, lifeguards and San Diego Fire Department searched all night.