The vote comes on the heels of a similar move last week in the House of Representatives.
The Republicans in recent weeks have also called for keeping the Guantanamo prison open.
Todd Kent, a professor of American politics at Texas A&M University, said that the political wrangling was making it difficult for Obama to fulfil his campaign pledge to close Guantanamo.
"The reason he doesn't have a lot of options is that no other country wants to take these prisoners and his own party, the leaders in congress, don't want them in their states," he told Al Jazeera.
"So it's forced, really, his hand back to the Bush administration policies."
But he said that while the political row might prove difficult for the president to negotiate, Obama was unlikely to see his standing with the public dented.
"He remains immensely popular [with the US public] ... but what it does is it exposes the Republican strength in national security."
The White House said after the vote that Obama would reveal details of his plans for the prisoners in a speech on national security on Thursday.
|There are concerns over the security risks of bringing the detainees into the US [EPA]
"The president understands that his most important job is to keep the American people safe and that he is not going to make any decision or any judgment that imperils the safety of the American people," Robert Gibbs, the White House press secretary, said.
Gibbs said Obama had not decided where some of the detainees would be sent but added that the president "understands that there aren't any easy decisions in this" but was determined to work with congress to fulfil his pledge to shut the place down.
Wednesday's vote drew criticism from the Pentagon which said legislators were making it "exceedingly difficult" to meet the president's January deadline.
The senate's vote, however, is not the final word on the matter.
Congress is expected to complete work on the legislation next month, giving the White House time pursue a compromise that would allow Obama to fulfil his pledge.
Earlier the head of the FBI told a congressional panel about the risks involved in bringing Guantanamo detainees into the US.
"The concerns we have about individuals who may support terrorism being in the United States run from concerns about providing financing to terrorists, radicalising others with regard to violent extremism, the potential for individuals undertaking attacks in the United States," Robert Mueller, the FBI's director, said.
"Guantanamo is used by al-Qaeda as a symbol of American abuse of Muslims and is fanning the flames of anti-Americanism around the world"
Dianne Feinstein, Democratic senator
Mueller said the threat of Guantanamo detainees radicalising others would apply even if they were held in supermaximum-security prisons on the US mainland.
Also this week, John Bates, a US district judge, ruled that some of the prisoners could be held indefinitely at Guantanamo without being charged, increasing the pressure on the Obama administration to develop a plan.
The overwhelming senate vote against Obama's plan was a victory for the Republicans, but Obama's Democratic allies, even in voting to deny the funds to close the detention facility, insisted the president was fundamentally correct.
"Guantanamo is used by al-Qaeda as a symbol of American abuse of Muslims and is fanning the flames of anti-Americanism around the world," Dianne Feinstein, a Democratic senator, said.