Victoria Police on Wednesday confirmed they discovered the remains of the 30-year-old camera operator, Surrey Hills man James Rose, and 56-year-old pilot Stephen Gale, of Brunswick.
Crews on Monday evening found the wreckage of the plane off the shore of Mornington.
Police alerted the public to the find on Tuesday, with divers later searching the wreckage in what officers described as a "complex recovery".
The downed aircraft was one of two Viper S-211 Marchetti planes doing a formation flight for a Jetworks Aviation promotional video about 12km west of Mount Martha.
They collided mid-air and one crashed into the water about 1.45pm on Sunday while the second landed safely at Essendon Airport with two people on board, including off-duty Qantas captain Joanne Mein.
It is understood Ms Mein was in the rear seat of the second aircraft and wasn't flying the jet.
Mr Gale, a highly experienced flyer, owned Jetworks Aviation, an Essendon Fields-based business created for the yet-to-air TV documentary Any Fool Can Fly.
The series was set to show a "group of high achievers" attempting to master flying, aerobatics and formation, with Australian comedian Tommy Little among the "student pilots" featured.
The business hosted flight training and joy rides, with one package offering a 45-minute two-jet fighter formation flight.
Mr Rose, a well-known and experienced drone operator who lived in Surrey Hills, has worked on high-profile TV shows for the Nine and Seven Networks and production company EndemolShine, including on cooking show MasterChef.
Police continue to investigate the crash and believe the aircraft would have been visible from Mount Martha between 1pm and 2pm on Sunday.
They again on Wednesday urged anyone with information about the incident to come forward.
The Australian Transport Safety Bureau is also investigating the crash.
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