The ship had just completed a secret mission delivering components of two nuclear weapons that would soon be used on Hiroshima and Nagasaki, Japan.
Allen said that the discovery was a humbling experience and a means of honoring sailors he saw as playing a vital role in ending World War Two.
The cruiser was en route from Guam to Leyte with over a thousand sailors and Marines on board when it was torpedoed and sunk by Japanese submarine I-58 on July 30, 1945, according to the Naval History and Heritage Command.
'As Americans, we all owe a debt of gratitude to the crew for their courage, persistence and sacrifice in the face of horrendous circumstances'. At over 18,000 feet down in the ocean, it also comes close to matching world records for deepest known wreck, which is now held by the World War II-era German blockade runner SS Rio Grande at 18,900 feet.
USS Indianapolis Survivor, and Vice-chairman of the Survivors' organization, Dick Thelen, 90, was absolutely surprised by the news that his ship had been located. The information led the research team to a new position and estimated search area for Allen's team.
In popular culture, the most well-known reference to the USS Indianapolis comes from "Jaws" when actor Robert Shaw, whose character Quint is depicted as a survivor of the incident.
Only 317 of those aboard the ship survived.
United States warship Indianapolis found 18000 feet deep in Philippine Sea
Identification was easier than in some deep-sea expeditions: some of the exposed wreck was clearly marked with Indianapolis signage, according to photographs shared by Allen and the Navy. "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", he said.
"Even in the worst defeats and disasters there is valor and sacrifice that deserves to never be forgotten", Sam Cox, director of the Naval History and Heritage Command, said in a statement, USA Today reported. The first was a 250-foot research vessel that Allen bought previous year and retrofitted with state-of-the-art subsea equipment, including a remote-controlled vehicle with attached HD cameras capable of diving 6,000 meters.
Others have tried to locate the Indianapolis before. "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-led expeditions have also resulted in the discovery of the Japanese battleship Musashi (March 2015) and the Italian WWII destroyer Artigliere (March 2017).
The 13-person team will continue to survey the site and tour the wreckage in compliance with relevant USA law for searching war graves.
The exact location of the sunken ship remained a mystery despite several searches for the wreckage over the years.