Two C-130 planes plus a charter aircraft took off from Juba "carrying non-emergency chief of mission personnel, private US citizens, and third country nationals," deputy State Department spokeswoman Marie Harf said in a statement.
The three groups were all "safely and successfully evacuated," she added.
"The security situation was getting ugly. There was shooting at the airport," said a defence official, who spoke on condition of anonymity, asked why the evacuations had gone ahead so swiftly.
The two C-130s came from Djibouti and landed in Nairobi about 1300 GMT, Pentagon spokesman Colonel Steve Warren said.
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South Sudan's President Salva Kiir offered today to hold talks with his arch-rival whom he accuses of leading a coup bid that has sparked days of fierce fighting in the world's youngest nation.
Hundreds of people have been killed and thousands more terrified civilians have fled their homes to UN bases since fighting erupted on Sunday.
The United States was "deeply troubled" by the outbreak of violence in the country, which it helped found in 2011 when it split from Sudan, Harf said, adding "it is absolutely critical that political differences be resolved by peaceful and democratic means."
Americans were still urged to leave the country and the State Department would "work to arrange for additional transportation as necessary to accommodate demand, taking into account security conditions and availability of regular commercial flights.