The search began when police received a distress call about 6pm from the man, who reported that his boat was taking on water.
Despite poor visibility, Water Police and the Police Air Wing launched a search operation to locate the man and his boat.
The man was found sitting on the upturned hull of his vessel about 11pm.
A marine rescue vessel was directed to the location and rescued the man from the water.
The man was wearing a life jacket and was uninjured.
He was taken to land by Fremantle Marine Rescue where he was reunited with his family.
Police have urged the public to remember the importance of always wearing a life jacket and carrying a registered, up-to-date EPIRB with GPS-enabled tracking to help alert authorities in emergency situations.