The Kyrgyz parliament passed the bill to shut the base by 78 out of 81 votes on Thursday.
The closure was announced last month after Russia offered $2.15bn in aid and loans for Kyrgyzstan's weak economy.
Russia and Kyrgyzstan both said that the closure of the air base was not a condition of the aid.
Bakiyev complained at the time that the US was not paying enough in rent for the base.
The US remains hopeful that the base may be reopened in the future, indicating that negotiations on the amount paid for its maintenance could be held.
Robert Gates, US defence secretary, said in Poland: "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."
"We're prepared to do something that we think is reasonable," he said.
The US pays $17.4m annually for the base, which was opened just after its offensive in Afghanistan began in 2001, following the September 11 attacks.
Closure of the Manas base would remove the last US air base from central Asia.
Uzbekistan closed a base on its territory in 2005, following western criticism of the government.