Two fishermen picked up the Australians, who waved for help while clinging to a life buoy, about 50 miles off a popular surfing town in Surigao province on Sunday.
Police in the provincial capital of Tandag said the men had been in the water for several days after the holed yacht capsized near the southern island of Mindanao while sailing to Subic Bay.
“Unfortunately, Anthony John Mahoney did not make it as he was already unconscious at the time of the rescue,” said police official Evelyn Tidula.
The Australian embassy in Manila is to help repatriate Mahoney’s remains, while the other two are in stable condition in hospital.
One of them has an address in the country’s north.
Police did not immediately explain how the yacht developed a hole.
The Australian Maritime Safety Authority alerted Philippine rescue authorities after detecting a distress beacon on Thursday and Friday last week, the agency said in a statement.
The Philippine Coast Guard said it found the wreckage of the Sydney-registered yacht at a beach on the Dinagat islands in Leyte Gulf, hundreds of miles from where the Australians were picked up.