The closure of the airport prompted speculation that the United States was deploying special forces in preparation for an attack against the militants who were involved in the attack.
A Libyan official said the spy planes flew over the embassy compound and the city, taking photos and inspecting locations of radical militant groups who are believed to have planned and staged the attack on the U.S. consulate on Tuesday.
Militants used anti-aircraft guns to fire at the drones, forcing the authorities to shut the airport because they feared for the safety of passenger planes.
"Two American drones flew over Benghazi last night with knowledge of the Libyan authorities," Deputy Interior Minister, Wanis al-Sharif told Reuters.
"They were visible to the eye, and came under attack by anti-aircraft weapons used by armed militias."
"For this reason, Benghazi security decided to close down the Benghazi airport air space. Any decision to allow an operation of any sort on Libya soil will be made in coordination with the congress and the new government."
Ambassador Christopher Stevens and the other Americans died after gunmen attacked the lightly fortified U.S. consulate and a safe house refuge in Benghazi on Tuesday night. The attack, which U.S. officials believe could have been planned in advance, emerged from a protest blaming America for a film they said insulted the Prophet Mohammad.
At least four international U.N. staff running the United Nations mission in Benghazi pulled out on Friday for security reasons, a U.N. source said.
Several Western diplomats including the Italian consul have also left the city, according to Libyan officials.
Ali al-Shaikhi, spokesman for the Army Chief of Staff said Western allied forces, who helped Libyan rebels to overthrow Muammar Gaddafi last year, continued to fly planes and drones over Libyan air space to help Libya keep its skies safe.
He said that they had increased flights in the past few days due to the worsening security situation.
"News came out that there were American drones in the air and so the airport received threats from unknown groups that they would attack any American planes circling over Benghazi. This led the airport to take the decision to close the air space to take precautions."
The U.S. military was moving two warships toward the coast of the North African state, giving the Obama administration flexibility for any future action against militant threats.
But a member of the Libyan national assembly told Reuters: "The Americans may have spoken to our President or Chief of Staff to coordinate an attack on the radical groups in Benghazi but they have not approached us as a congress (assembly) yet."
"I believe that so far we as Libyans can take care of the operation ourselves because the militias feel they are part of Libyan society, but if we have Americans come in with an operation then these militias will also turn on us," he said.
"For sure we will need the Americans for their logistical and technical support and expertise, and we will ask them for it when the time comes. But for now we need to try to do it ourselves."
Airport manager Taba Mohammed said the closure ran for about 10 hours from 2030 EDT. U.S. officials said earlier a Marine Corps anti-terrorist squad was being sent into Libya to shore up security.
"We have now reopened the air space. It was closed for routine security checks," Mohammed told Reuters.
Turkish Airlines said the closure of Benghazi air space had forced one of its flights with 121 people aboard to turn back to Istanbul on Friday.
President Barack Obama has vowed to bring to justice those responsible for the Benghazi attack, which U.S. officials said may have been planned in advance. Secretary of State Hillary Clinton said Washington had nothing to do with the video, which she called "disgusting and reprehensible".
The United States and Libya have agreed to cooperate closely in investigating the attack in Benghazi, a hotbed of anti-Western Islamists, some with links to al Qaeda, since the fall of dictator Muammar Gaddafi in a popular revolt last year.
Abdul Salam al-Barghathy, a senior security official in Benghazi, told Reuters that the team investigating the U.S. attack "had identified those responsible."
"But we are continuing our interrogations to reach conclusive information" he added.
Libyan security officials believe that Ansar al-Sharia and members of al Qaeda's north Africa-based affiliate, known as Al Qaeda in the Islamic Maghreb, may have been involved in the attack. They both want Islamist Sharia to be implemented in Libya and reject Libya's U.S.-backed bid for democracy.