In a letter to Congress, Obama said he could take further action to protect Americans.
The State Department said Americans were flown out on U.N. and U.S. civilian helicopters.
The president warned fighting leaders to negotiate differences or risk losing U.S. support.
Gunfire hit their aircraft during a mission to evacuate Americans in South Sudan.
The measure must still be signed by President Yoweri Museveni to take effect. The president has said there will be further “consultations” before a decision is made.
The State Department said citizens departed on three flights amid an outbreak of violence.
Americans in South Sudan are advised to “depart immediately."
The Pentagon is considering whether to begin a large-scale training mission with Libya, in an effort to help stabilize the security situation in the country.
The plan under consideration by the White House would have U.S. forces train nearly 8,000 Libyan troops, molding them into a "general purpose" force designed to tackle missions ranging from counter terrorism to basic security operations.
McCain backed off comparison of Obama-Castro handshake to Chamberlain and Hitler.
"Today marks the end of an extraordinary journey," South Africa's president said.