During its later life as a supply ship, the Terra Nova was damaged by ice in 1943 and sank off the tip of Greenland.
Its crew was rescued by the United States Coast Guard.
The wreckage remained unseen on the sea bed until last month when the Schmidt Ocean Institute stumbled across it while testing it equipment.
The Terra Nova was known to be in the area but its exact location was unknown.
The institute's echosounder technology discovered a boat-shaped object measuring 57m long, matching the dimensions of the Terra Nova.
A camera was sent down to more closely inspect and took photos of the wooden wreckage, which, when matched with historic photographs, confirmed the ship's identity.
Brian Kelly, the education officer at the Discovery Point Heritage Museum, told the Telegraph newspaper he was "amazed" by the discovery.
"It is remarkable that the Terra Nova has been found now, 100 years on from the race to the pole, the death of Scott and four of his crew, and in the year of various events to commemorate that occasion," he said.
"She was severely damaged when she was sunk by the US Coastguard and the front of her hull is peeled back, suggesting that the structure may not be able to take any movement."
Because of the depth the ship was found at, its condition, and the cost of any salvage operation, it was unlikely the wreck would be recovered, he said.