A survey of one site near the well in the Gulf of Mexico uncovered "compelling evidence" of pollution damage. Coral communities more than 1,220 metres (4,000ft) below the surface of the ocean appeared stressed and discoloured.
Tests showed that oil from the site bore Deepwater Horizon's chemical "fingerprint".
Determining the impact of oil spills at the bottom of the ocean can be difficult because oil seeps naturally from cracks in sea floor.
The explosion, in April 2010, poured an estimated 405m litres (160m gallons) of oil into the Gulf, causing a major environmental disaster.
Scientists looked at 11 deep-water coral sites three to four months after the well head was capped.
Healthy coral was found at all locations more than 12 miles from the Macondo oil prospecting site, where the blowout occurred. But at one site, seven miles south-west of the well, coral colonies presented "widespread signs of stress", including bleaching and tissue loss. Almost half of the 43 corals observed at that site showed evidence of impact.
The US scientists used an automated submersible, Sentry, and a manned robotic-armed vehicle, Alvin, to obtain images and samples at a depth of more than 1,300 metres. Their findings are published in the journal Proceedings of the National Academy of Sciences.
Professor Charles Fisher, from Pennsylvania State University, took part in the initial dive, by a remotely operated vehicle (ROV), which identified the site.
He said: "We discovered the site during the last dive of the three-week cruise.
"As soon as the ROV got close enough to the community for the corals to come into clear view, it was clear to me that something was wrong at this site. I think it was too much white and brown, and not enough colour on the corals, and brittle stars.
"Once we were close enough to zoom in on a few colonies, there was no doubt that this was something I had not seen anywhere else in the Gulf: an abundance of stressed corals, showing clear signs of a recent impact. This is exactly what we had been on the lookout for during all dives, but hoping not to see anywhere."
A second, more detailed look, including six dives by Alvin, confirmed the findings.
An advanced "fingerprinting" technique called comprehensive two-dimensional gas chromatography was used to determine the source of the oil.
The scientists wrote: "The presence of recently damaged and deceased corals beneath the path of a previously documented plume emanating from the Macondo well provides compelling evidence that the oil impacted deep-water ecosystems."