Crews aboard the Vulcan Inc's research vessel R/V Petrel found the remains of the vessel at a depth of 6,220m (20,400ft) on the bed of the Philippine Sea.
The ship is thought to be the USS Johnston DD-557, a Fletcher-class destroyer sunk during the Battle of Leyte Gulf off Samar in the Philippines on 25 October 1944.
The Battle of Leyte Gulf lasted three days and is considered one of the largest naval engagements in history, involving more than 200,000 naval personnel.
It was the last action between battleships in history and was the first battle in which Japanese aircraft carried out organised kamikaze attacks.
The Japanese navy suffered heavy losses and did not put to sea again in any force for the rest of the war, trapped in base by a lack of fuel.
According to the US navy, the USS Johnston, under Commander Ernest E Evans, was deployed to Leyte Gulf in the Philippine Sea on 20 October 1944. On 25 October, the ship took on heavy fire during a surprise attack from the Japanese Center Force.
According to the navy: "One by one, Johnston took on Japanese destroyers, although Johnston had no torpedoes and limited firepower. After two-and-a-half hours, Johnston - dead in the water - was surrounded by enemy ships.
"At 9.45 am, Evans gave the order to abandon ship. Twenty-five minutes later, the destroyer rolled over and began to sink."
Of the crew of 327, only 141 survived.
Vulcan Inc said the remnants of the destroyer were found 6,220 metres below the ocean's surface, "making this the deepest discovery of any warship in history".
It went on: "As with all their expeditions, the crew aboard R/V Petrel hope this discovery will bring a sense of closure for the families of those lost during this battle."
