The four-metre-wide fuselage was lifted out of the water by a crane and taken back to shore by barge on Saturday morning.
Stephen Gale, 56, and cameraman James Rose, 30, went down in one of two Viper S-211 Marchetti planes on Sunday during a formation flight.
They were filming a Jetworks Aviation promotional video about 12km west of Mount Martha when the planes collided.
The second aircraft was able to land safely.
Victoria Police confirmed on Wednesday the bodies of Mr Gale and Mr Rose had been found after crews located the wreckage of their plane off Mornington.
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.
Earlier this week comedian and media personality Tommy Little penned a tribute to Mr Gale, who was his mentor.
Little was among student pilots to be featured in the series about a group of high achievers attempting to master flying, aerobatics and formation.
The comedian remembered Mr Gale, a former Royal Australian Air Force member, as one of his closest mates and sidekick in the sky.
"An inventor, an adventurer and a heart of gold. He was a real life Tony Stark but with a flying suit instead of an iron one. His love for aviation was unparalleled," Little wrote on Facebook.
Terribly sad to hear of the tragic deaths of Stephen Gale & James Rose over Port Phillip Bay. I was a passenger on a flight with Stephen some years ago at Mt Hotham. It's an experience I'll never forget. Always smiling, professional & inspiring. Thanks for the memories, Stephen. — Anthony Carbines MP (@ACarbinesMP) pic.twitter.com/oRRwLxP00oNovember 20, 2023
The Australian Transport Safety Bureau will now examine the plane.
Police are investigating the cause of the collision.
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