Ahmed Abu Khatallah was arrested on June 15, Pentagon Press Secretary, Rear Admiral John Kirby said.
"He is in US custody in a secure location outside of Libya. There were no civilian casualties related to this operation, and all US personnel involved in the operation have safely departed Libya," Kirby said in a statement welcomed by Americans but also seen as a major development in bringing to justice the perpetrators of the terrorist strike.
Obama said he recently authorized an operation in Libya to detain Khatallah for his role in the attacks.
The fact that he is now in US custody is a testament to the painstaking efforts of US military, law enforcement, and intelligence personnel, he said.
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Four American nationals, including the then US Ambassador to Libya, Chris Stevens, were killed in the attack on the US consulate in Benghazi on September 11, 2012.
"With this operation, the United States has once again demonstrated that we will do whatever it takes to see that justice is done when people harm Americans. We will continue our efforts to bring to justice those who were responsible for the Benghazi attacks," said the US President.