The Marin County Sheriff's Office identified the sailor as Andrew Henry Ewing, 31, of Sacramento.
Ewing had set course for the Philippines just hours before the U.S. Coast Guard received a distress signal, officials said.
The lone passenger on a 30-foot sailboat named the Alma, Ewing set out from a dock in Alameda on Sunday.
Early Monday, the Coast Guard received an alert from the sailboat that sank off the rocks near the Golden Gate Bridge and prompted a search.
Deputies said Ewing's body washed ashore on the southwest side of Angel Island, where a U.S. Coast Guard helicopter crew spotted him Tuesday.
The body was taken to a Coast Guard station and turned over to the Marin County coroner. Fingerprints were used to confirm his identity.
The coroner's office said it will continue to investigate, but foul play was not suspected.