The fisherman was 95 nautical miles east of Townsville when the dory overturned about 8am on Sunday, 19 June.
The man activated a flare as he passed by the mother ship, which went unnoticed due to poor visibility in the area.
An Emergency Position Indicating Radio Beacon (EPIRB) was then activated.
AMSA Search and Rescue received the beacon detection about 10.30am and tasked its Cairns-based search and rescue plane to respond.
It also tasked an Australian Border Force plane, which spotted the overturned vessel and stayed overhead.
Townsville based helicopter Rescue 521 arrived in the area, winching the fisherman to safety about 12.40pm.
The beacon was correctly registered with AMSA, which provided search and rescue officers with vital information to assist in the coordination of the search and rescue.
AMSA urges all beacon owners to register their beacons online or by calling 1800 406 406.