The cruiser had just finished a high-speed mission to move parts for "Little Boy" - the atomic bomb used on Hiroshima - from California to Tinian, a Pacific island home to a key air base during the war.
The story of the Indianapolis was the subject of the 2016 movie staring Nicolas Cage - "USS Indianapolis: Men of Courage" - which was filmed in Mobile, using the museum World War II battleship USS Alabama for many scenes.
A team of civilian researchers has discovered the wreck of the USS Indianapolis, a US Navy cruiser which Imperial Japanese forces sunk in July 1945 to the loss of almost three quarters of its crew.
Reports say that the wreckage was found at a depth of 18,000 feet in the Pacific Ocean.
The sinking of the USS Indianapolis remained unknown to the Navy for several days.
Paul Allen, the Microsoft co-founder and owner of the Seattle Seahawks, led a search team to find the ship. "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".
Only 316 members of the crew survived while the other 880 sailors and Marines died either when the boat sank or after spending days in the water.
Its loss seventy-two years ago - punctuated by the subsequent harrowing tale of its survivors and their delayed rescue - is one of the great naval tragedies of World War II and American naval history.
Seven-plus decades after the sinking of the Indianapolis, the wreckage was found resting on the seafloor Saturday by a team that included historians from the Naval History and Heritage Command in Washington, D.C.
Researchers with Allen's organization were able to locate the ship in part because of a naval landing craft that had recorded a sighting of the USS Indianapolis the night that it was torpedoed, using the coordinates to get a location on the ship.
"Even in the worst defeats and disasters there is valor and sacrifice that deserves to never be forgotten", said Sam Cox, director of the Naval History and Heritage Command.
'They can serve as inspiration to current and future Sailors enduring situations of mortal peril. The wreck was located by the expedition crew of Allen's Research Vessel Petrel, a 250-foot vessel equipped with state-of-the-art equipment capable of diving to 6,000 meters, or 3 1/2 miles. "We've assembled and integrated this technology, assets and unique capability into operating platform, which is now one amongst very few on the planet".
Allen's team is still surveying the site of the wreckage and plans to conduct a live tour of the wreckage in the next few weeks. The USS Indianapolis remains the property of the U.S. Navy and its location will remain confidential and restricted by the Navy. The new search area still comprised 600 square miles of open ocean.