Vanity Fair magazine had reported Mark Felt admitted being the source whose identity had been secret for decades.
The scandal forced the resignation of Republican President Richard Nixon in August 1974.
Deep Throat helped Washington Post reporters Bob Woodward and Carl Bernstein uncover the Watergate affair.
Initially the reporters refused to confirm Mr Felt's identity.
"We've said all along that when the source, known as Deep Throat, dies, we will reveal his identity," said Bernstein, according to MSNBC.
But later on Tuesday, Woodward said Mr Felt was indeed Deep Throat, in a statement carried on the Washington Post's website.
"It's the last secret" of the story, said Ben Bradlee, who was the Washington Post's senior editor at the time.
Mr Felt, now 91, told Vanity Fair: "I'm the guy they used to call Deep Throat."
The name derived from a famous pornographic film of the time.
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