The official said that El Shafee Elsheikh and Alexanda Amon Kotey were captured in early January in eastern Syria.
He appeared in a number of videos slaughtering hostages including British aid workers David Haines and Alan Henning.
The group was nicknamed the Beatles due to their English accents.
Aine Davis, the fourth member, was detained in Turkey in 2015 and convicted on terror charges previous year.More news: ESPN Plus streaming service announced for Apple devices
The newspaper said the U.S. troops confirmed their identities using fingerprints and additional biometric measurements.
A statement confirmed they were suspected of the "detention, exploitation and execution of Western detainees. and are thought to have links to the British terrorist often called Jihadi John".
The New York Times said that the SDF caught the men in January and have made them available to the United States military personnel for questioning.
Under interrogation they gave up "valuable information" on Islamic State's remaining leadership and structure, the newspaper reported.
Former child refugee Elsheikh was a mechanic from White City in West London, and Alexanda Kotey was from Paddington.More news: Cavaliers trading Thomas to Lakers for Nance, Clarkson
The Telegraph past year reported that the two missing men were on a USA "kill list" reserved for senior Islamic State terrorists.
The state department says that Kotey "likely engaged in the group's executions and exceptionally cruel torture methods, including electronic shock and waterboarding". Mr Cantlie appeared in a string of Isis propaganda videos.
However, the presence of large numbers of Kurdish armed forces in northern Syria has alarmed neighbouring Turkey.
Born in 1983, Kotey was also connected to the "London Boys" - a network of extremists who fomented radical Islam while playing five-a-side football in west London and who were linked to the 7/7 London bombings and the subsequent failed 21/7 plot.
In May 2017 he was jailed for seven and a half years by a Turkish court for being part of a terror organisation.More news: Winter weather could make for slick afternoon commute
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