Parliament voted overwhelmingly on Thursday in favour of the bill to close the Manas air base outside the Kyrgyz capital, with 78 out of 81 lawmakers present voting in favour. One MP voted against and two abstained.
The US military will have 180 days to remove its soldiers and equipment from the base once it is officially notified by the government.
Bakiyev's announcement last month of the closure came after Russia offered more than $2 billion (Dh7.4 billion) in aid to the struggling Kyrgyz economy. The government has insisted that Moscow did not set the closure as a condition.
US Defence Secretary Robert Gates said in Poland that the US would not pay beyond a "reasonable" amount to use the Manas base and said the vote would not be "the last word."
"I think we are prepared to look at the fees and see if there is a justification for a somewhat larger payment but we're not going to be ridiculous about it," he said.
"We're prepared to do something that we think is reasonable."
The United States pays $17.4 million a year to use the strategic air base, which serves as a vital hub for moving troops and supplies in and out of Afghanistan.