The wreckage was found in the Philippine Sea 5.5 kilometres below the surface, according to philanthropist Paul Allen, who headed the civilian research crew that located the ship.
The ship was hit in the final days of World War II just after completing a secret mission delivering parts of the atomic bomb used in Hiroshima.
The vessel sank in just 12 minutes, meaning it was unable to send a distress signal or deploy life-saving equipment, according to the history division of the US Navy.
"To be able to honour 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," said Allen.
"As Americans, we all owe a debt of gratitude to the crew for their courage, persistence and sacrifice in the face of horrendous circumstances."
Allen's team is currently surveying the full site and plans to give a live tour of the wreckage in the coming weeks. Since the sunken vessel is a war grave, it is protected by US law from being disturbed.
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