One of the backers, Sen. James Inhofe, defended the treatment of Guantanamo detainees and said one of their biggest problems was obesity.
"They're eating better than they've ever eaten at any other time in their life," Inhofe said.
The stalemate leaves language in the defense bill that only slightly advances Obama's cause. The White House has called the bill constructive while insisting that more be done to provide officials with the necessary flexibility to close the prison.
Any final law needs the Republican-led House of Representatives' support, and such a scenario is highly unlikely.
Obama's effort to loosen restrictions on Guantanamo detainees faces dogged resistance, with opponents citing the cases of some suspects who've been released to foreign countries only to later join terrorist efforts.
Earlier this year, the House banned sending detainees to Yemen, where more than half the remaining detainees come from. Yemen is also home to perhaps al-Qaida's most active branch.
Obama established his own ban on Yemeni transfers after a Nigerian man tried to blow up a U.S.-bound flight on Christmas four years ago with explosives hidden in his underwear. The bombing instructions came from al-Qaida operatives in Yemen.
Obama lifted the moratorium in May, calling Guantanamo a "symbol around the world for an America that flouts the rule of law."
Senate advocates of closing Guantanamo repeatedly cited the high cost of maintaining the facility: $2.7 million a year per prisoner.
Total spending on Guantanamo amounts to $454 million a year, according to the Defense Department.
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Associated Press writer Bradley Klapper contributed.