Colonel John Blashford-Snell found the cast-iron submarine, named Explorer, half-submerged in three metres of water off the coast of Panama.
Like Nautilus, the craft is cigar-shaped and has a lock-out system, which allows submariners to leave, collect items from the seabed and then return to the vessel.
It was built in 1864, five years before Verne's classic adventure story was published, and it is thought that the French writer would have read about the sub's specifications.
Col Blashford-Snell, 67, who runs the Dorset-based Scientific Exploration Society, heard about the object 20 years ago. At first he was told she was a Japanese mini-sub but someone else insisted it was just an old boiler so he forgot about it.
But when he returned to Panama recently looking for ancient ruins, a maritime museum in Canada asked him to examine the object.
"We were very lucky to find it because at high tide it is totally submerged, but we got there at low tide when about half of it is showing," he said.
"We waited until high tide so we could dive on it properly and do a full survey. It was quite an experience because we had an expert with us who said it was much earlier than we had thought and dated from the American civil war."
The 10-metre long vessel was built by a visionary inventor called Julius Kroehl for the Union forces but it was not used in the war. It ended up in Panama where the lock-out system made it a useful tool in the pearl trade.
"I realised it was identical to the system used in Nautilus," Col Blashford-Snell said, adding that Verne must have read about the Explorer's lock-out system and used it in his book.
The Explorer was abandoned after all its crew died of what was reported to be a fever but may well have been the bends.
One of Britain's most noted maritime heritage experts, Wyn Davies, agreed that the Explorer may well have inspired Verne.
"If Jules Verne was researching the relatively new world of submersible vessels, he would probably have heard of the Explorer's lock-out system," he said. "Submarine inventors were keen to sell their products so there would have been none of today's secrecy and technologies would have been keenly scrutinised on both sides of the Atlantic.
"As far as I'm aware the Explorer possessed the world's first lock-out system and its very uniqueness might have stimulated Verne's imagination.
"The cigar shape is also a clue that Verne might have borrowed his concept from the Explorer because other submersibles of this era came in a variety of shapes."
June 6, 2005
The Guardian Unlimited