Ahmed Abu Khattala was taken into custody in a secret US military raid in Libya on June 15.
He is now being held in a secure location outside the country, a Pentagon spokesman confirmed.
US Ambassador Chris Stevens and three others were killed in the attack.
“There were no civilian casualties related to this operation, and all US personnel involved in the operation have safely departed Libya,” Pentagon press secretary Rear Adm John Kirby wrote in a statement.
After the announcement, President Barack Obama praised the courage and professionalism of the military, law enforcement and intelligence personnel who tracked and captured Ahmed Abu Khattala, who the US describes as a “key figure” in the attack.
“With this operation, the US has once again demonstrated that we will do whatever it takes to see that justice is done when people harm Americans,” he said in a White House statement.
Ahmed Abu Khattala would face the “full weight of the American justice system”, he said, an indication the US will try him in a civilian court rather than hold him at the military detention centre at Guantanamo Bay, Cuba.
In August, the New York Times reported that federal prosecutors had prepared secret charges against him, accusing him of murder for his role in the attack.
On September 11, 2012, gunmen stormed the US consulate in Benghazi and set it on fire.
In addition to Chris Stevens, information technology specialist Sean Smith and security workers and ex-Navy Seals Tyrone Woods and Glen Doherty were killed.
The White House initially said the attack stemmed from anti-American protests over a crude video produced in the US that was deemed insulting to Islam.
Government investigators soon determined it was an organised attack planned by local militias, although the New York Times claimed after an extensive investigation that some of the attackers were indeed motivated by the film.
The US quietly offered as much as $10 million for information in the months following the attack.
In subsequent years, the incident has become a political lightening rod, with Republicans accusing President Barack Obama’s administration of covering up the involvement of militant groups in the days after the attack in order to assist Obama’s 2012 re-election campaign.
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