Obama responded to the defeat by saying he will push to get pieces of his bill enacted.
"Tonight's vote is by no means the end of this fight," he said in a statement released by the White House, adding he will work with Senate Majority Leader Harry Reid of Nevada "to make sure that the individual proposals in this jobs bill get a vote as soon as possible.
"In the coming days, members of Congress will have to take a stand on whether they believe we should put teachers, construction workers, police officers and firefighters back on the job. They'll get a vote on whether they believe we should cut taxes for small business owners and middle-class Americans, or whether we should protect tax breaks for millionaires and billionaires.
"With each vote, members of Congress can either explain to their constituents why they're against common-sense, bipartisan proposals to create jobs, or they can listen to the overwhelming majority of American people who are crying out for action."
Sens. Ben Nelson of Nebraska and Jon Tester of Montana were the only Democrats to vote with Republicans in sinking the measure 50-48, The Hill reported.
The vote was held open to give Sen. Jeanne Shaheen, D-N.H., time to return to Washington after receiving a civic honor in Boston. Sen. Tom Coburn, R-Okla., didn't vote for medical reasons, The Hill said.
"The truth of the matter is, most Democrats know just as well as I do that passing another stimulus and tax hike is a lousy idea -- which is why the president is having such a hard time convincing many Democrats to vote for it," Senate Minority Leader Mitch McConnell, R-Ky., said before the vote.
While he stuck with his party, Sen. Jim Webb, D-Va., said he is against raising taxes on ordinary income, particularly when the economy is faltering.
"I strongly believe that the way to bring good jobs back is to improve our economy in the private sector and that means more capital investment," Webb said. "Winston Churchill once said something to the effect that you can't tax your way out of an economic downturn any more than you can pick up a bucket if you're standing in it."
Obama had met Monday with Senate Democratic leaders to plan the next steps after Tuesday's vote.
A White House official told The Hill Obama and Senate Democrats are "clearly on the same page going forward" and they will work together "to sequence out which components and when" to move them in the days ahead."
The jobs bill includes $175 billion in public-works spending, unemployment benefits and aid to states to avoid teacher layoffs, the Times said.
The president also has proposed a national infrastructure bank, which some Republicans might support in exchange for repatriating corporate profits at a lower tax rate.
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