The USS Indianapolis was torpedoed by a Japanese submarine in the early hours of 30 July, 1945.
It sank in just 12 minutes, before the crew could send a distress signal or deploy life-saving equipment.
Around 800 of its 1,196 sailors survived the sinking but most of them fell victim to sharks or dehydration.
Only 316 sailors were alive four days later when a passing bomber spotted them and a rescue began.
Just 22 of them are still living today, the US Navy said.
The ship’s loss came just after it completed what turned out to be its final mission: delivering parts of the atomic bomb that would be used to devastate the Japanese city of Hiroshima and ultimately force Japan out of the war.
Its story became the theme of many books and films, including USS Indianapolis: Men Of Courage, starring Nicolas Cage.
It was also mentioned in Stephen Spielberg’s Jaws of 1975, with fictional survivor Captain Quint remembering his wait to be rescued after the disaster.
But 72 years after it sank, the wreckage of the USS Indianapolis has been found in the Philippine Sea by 13 civilian researchers on the Research Vessel Petrel.
The ship lies 3.5 miles below the surface, according to philanthropist Paul Allen, who headed the team.
Mr Allen, also co-founder of Microsoft, said in a statement released by the US Navy that the discovery was “humbling”.
He said: “To be able to honor the brave men of the USS Indianapolis and their families through the discovery of a ship that played such a significant role in ending World War II is truly humbling.
“While our search for the rest of the wreckage will continue, I hope everyone connected to this historic ship will feel some measure of closure at this discovery so long in coming.”
Mr Allen has led expeditions to find other warships in the past and in August 2015 his team also found and restored the ship’s bell from HMS Hood.
It was later presented to the Royal Navy.
Mr Allen’s team is not the first to search for the USS Indianapolis but his success has been put down to his re-fitting of the Research Vessel Petrel with state of the art equipment capable of diving to 3.5 miles, or 6,000 metres.
The other key factor was the discovery of a new search position, the result of research by historian Dr Richard Hulver, at the Naval History and Heritage Command.
The expedition will survey the site and do a live tour in the next few weeks.
The ship remains US property and its exact location will not be revealed, the Navy said.
US law also says that the wreck is to be respected as a war grave and must not be disturbed, a law that the Navy said had been followed by the researchers.
Sam Cox, director of the Naval History and Heritage Command, said: “Even in the worst defeats and disasters there is valour and sacrifice that deserves to never be forgotten.”