US Central Command spokesman Maj John Redfield would not give a specific reason for the temporary suspension, adding that it was taken by US military at the Masas base, just outside the Kyrgyz capital.
Russia also has an airbase in Kyrgyzstan, and the presence of both has been the focus of debate in recent months.
The US base at Manas is crucial to its operations in Afghanistan - 50,000 coalition troops passed through the base in March - but its lease is due to expire in July.
Mr Bakiyev told the BBC the opposition wanted to close the base down.
"I think that would be wrong. It's really vital, not only for America but also for Kyrgyzstan and for the whole of Central Asia," he said.
But Ms Otunbayeva said on Friday: "We will not touch the airbase. The existing contracts will remain in place."
The BBC's Richard Galpin says that in order to avoid being followed, the ousted president was taken in several different vehicles by security guards to his modest new home in Jalalabad.
AT THE SCENE
Rayhan Demytrie BBC News, Bishkek
Hundreds of people gathered in Bishkek at the scene of Wednesday's mass protests. A little shrine was set up by the main gates to the presidential office, known as the White House. Blood still stains the ground where the flowers were laid. People sat down for mass prayers. One mourner said that lots of young men had sacrificed their lives for the country and today they were being mourned.
Two days on, the situation in Kyrgyzstan is slowly getting back to normal. Many are referring to Wednesday's events as their own people's revolution. What they're hoping for most is that the new government will make better decisions, create more jobs and prioritise the nation's prosperity more than their own.
The small city is in southern Kyrgyzstan, Mr Bakiyev's power base.
Mr Bakiyev said he feared those responsible for the uprising in the capital on Wednesday were trying to track him down.
He said the uprising was a well-organised, covert operation in which there was foreign involvement, although he refused to say which country.
Mr Bakiyev said his office in Bishkek had been riddled with bullets on Wednesday in an attempt to kill him and that although he regarded himself as the legitimately elected president, with widespread support, he could not go back.
"If I were to turn up in Bishkek today I would not be safe. I would be killed, or they would throw me into the crowd saying, 'This is the man who ordered the police to open fire, he is responsible for the bloodshed'," he said.
Mr Bakiyev said he would stay in the country to prevent civil war that could erupt because of the deep divide between the north and the south of the country.
He also poured scorn on the interim government set up by the opposition, saying it was unable to restore law and order.
Funeral for uprising victim in Bishkek
He added that he and his ministers were continuing to work in order to stabilise the country.
Mr Bakiyev has offered to talk to the opposition but Ms Otunbayeva says she has no plans to do so and says Mr Bakiyev must resign.
Kyrgyzstan on Friday observed a day of national mourning for the victims of the protests, with the first funerals being held.
Thousands of mourners gathered in the main square of Bishkek.
Many of them blamed the deaths on Mr Bakiyev.
"Bakiyev must be tried and executed for all these crimes," said Fatima Imanaliyeva, whose two friends were killed when security forces opened fire on protesters.
TIMELINE: KYRGYZSTAN UNREST
March 2005: Protests over disputed parliamentary election, dubbed the Tulip Revolution, lead to fall of President Askar Akayev; Kurmanbek Bakiyev appointed acting president and PM
July 2005: Mr Bakiyev elected president by a landslide
May 2006: Mass protests demand constitutional reform and more action to combat corruption
October 2007: Referendum approves constitutional changes, which the opposition present as a step towards authoritarianism
December 2007: Mr Bakiyev's Ak Zhol party wins parliamentary poll; opposition left with no seats
July 2009: Mr Bakiyev re-elected in vote criticised by monitors
January 2010: Opposition leader Ismail Isakov jailed for eight years for corruption, sparking opposition hunger strikes
April 2010: Clashes between police and anti-government protesters leave 75 dead
"We will never forgive him. This is our revolution," she told Reuters news agency.
Another mourner, Azimbek Sariyev, told Associated Press: "My friend Talas perished. I hope he hasn't died for nothing. We have ousted Bakiyev and won't allow the rulers to mock us."
Ms Otunbayeva has accused Mr Bakiyev's supporters of continuing to orchestrate "incidents of violence" around the capital.
She said "several bombs" had been planted in Bishkek.
Russia appears to have given its backing to Ms Otunbayeva's leadership - she has already held telephone talks with Prime Minister Vladimir Putin.
The deputy head of the interim government, Almazbek Atambayev, has gone to Moscow "for talks on economic aid", the government said in a statement.
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