The remains of the vessel, the Two Brothers, was found in shallow waters off Hawaii.
Captain George Pollard was the skipper when the ship hit a coral reef and sank in 1823.
His previous ship, the Essex, had been rammed by a whale and also sank, providing the narrative for the book.
'Pretty amazing'
The remains of the Two Brothers were found by researchers from America's National Oceanic and Atmospheric Administration (Noaa), about 600 miles (965 km) north-west of Honolulu in the remote chain of islands and atolls.
The wooden vessel has disintegrated in the warm waters, but the researchers found harpoons, a hook for stripping whales of their blubber and cauldrons used to turn whale blubber into oil.
"To find the physical remains of something that seems to have been lost to time is pretty amazing," said Nathaniel Philbrick, an author and historian, who has been researching the Two Brothers, the Essex and their captain.
"It just makes you realise these stories are more than stories. They're about real lives."
The sinking of the Two Brothers was relatively uneventful compared with the Essex's run-in with the sperm whale in 1821.
After the Essex sank, Capt Pollard and his crew drifted at sea without food and water for three months and even resorted to cannibalism before they were rescued.
Pollard gave up whaling and became a night watchman in Nantucket, Massachusetts.
While Meville was inspired by Pollard's adventures, the unlucky seafarer's character is not thought to have been the basis for the novel's obsessive Capt Ahab.
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