The message forwarded to Clinton in January 2013 was from Tom Shannon, then US ambassador to Brazil.
The ambassador congratulated Clinton on her testimony before the Senate Foreign Relations committee about the attack, during which four Americans died.
The email was filed in court by the State Department today as part of a lawsuit by a conservative legal advocacy group.
Judicial Watch has filed numerous lawsuits seeking government documents involving the Democratic presidential nominee's tenure as secretary of state.
She and her lawyers deleted thousands of additional emails that were described as personal and private.
Some emails Clinton didn't turn over but were recovered by the FBI from other people's accounts were work-related.
The State Department said in court last week it had identified about 30 emails from the FBI haul that were potentially responsive to Judicial Watch's request for messages related to the Benghazi attack.
But after further review, the department said in its latest court filing that all but one of those were duplicative of emails already made public.
"I watched with great admiration as she dealt with a tough and personally painful issue in a fair, candid, and determined manner," Shannon wrote of Clinton's Senate testimony.
"I was especially impressed by her ability to turn aside the obvious efforts to politicize the events in Benghazi, reminding Americans of the tremendous sacrifice made by (US ambassador to Libya) Chris Stevens and his colleagues but also insisting that our ability to play a positive role in the world and protect US interests requires a willingness to take risks."
The email also does not support the supposition that Clinton and her lawyers deleted emails about Benghazi to hide evidence of wrongdoing.
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