US Navy spokesman Christopher Johnson said the wreck had been positively identified on Monday using a remote controlled submersible, CNN reported.
The US National Transportation Safety Board (NTSB) also confirmed the identification.
What was believed to be the wreck of the El Faro was first detected on 31 October at a depth of 15,000 feet, upright on the seabed.
The El Faro sank on 1 October, with 33 crew onboard, during Hurricane Joaquin. Rescuers have only recovered one body to date.
A salvage team will now seek to retrieve the ship's voyage data recorder.