Bakiyev said earlier this month that he had decided the air base should close because Washington had refused to pay more rent for it.
He announced his decision in Moscow after accepting more than $2bn in Russian aid and credit.
However, Kyrgyzstan's opposition has criticised the proposal and accused the president of caving in to Russian pressure to close the base.
"This $2bn has been paid in order to convince Kyrgyzstan to close the base," Bakyt Beshimov, an opposition politician, said.
"I am saddened by the fact that Kyrgyzstan's image has now been so seriously tarnished."
However, both Moscow and the Kyrgyzstan government have denied there is any connection between the Russian financial aid and credit package and the decision to close Manas.
The base, located outside the Kyrgyz capital Bishkek, had been set up to assist international forces in Afghanistan.
Kyrgyzstan's government has, however, long been unhappy over its prolonged presence.
Under the terms of the original deal Washington has six months to shut down the base if notified that Kyrgyzstan no longer wishes it to remain.
Following Kyrgyzstan's announcement, Russia said it would allow non-lethal US military supplies for Afghanistan to cross its territory.
The vote came amid rising concerns over how to secure supply routes to troops in Afghanistan and heightened rivalry between Washington and Moscow for control of central Asia.
David Petraeus, the commander of US forces in Afghanistan and Iraq, visited Uzbekistan, Kyrgyzstan's neighbour, on Tuesday in an attempt to secure alternative supply routes into Afghanistan for US forces.
Convoys travelling along Pakistani supply lines to Nato and US-led troops in Afghanistan have been frequently attacked, and the closure of the Manas base could cause further logistical problems.
Robert Gates, the US defence secretary, will also ask Nato allies to send extra troops to Afghanistan after Barack Obama, the US president, approved deploying an extra 17,000 US troops ahead of Afghan elections in August.
Nato defence ministers are due to meet in the Polish capital Krackow on Thursday.
"The message is that it is a new [US] administration and the administration... is prepared to make additional commitments to Afghanistan," Gates said.
"But there clearly will be expectations that the allies must do more as well."