It is believed the submerged boat was located by a fisherman about four nautical miles from Ricketts Point.
Water Police are towing the boat to Black Rock where it will be examined.
The 83-year-old and 56-year-old were last seen at 7am on 11 December at Olivers Hill boat ramp in Frankston.
The pair told family they were going on a trip for a couple of days on their boat, registered ER422.
The search for the pair continues.