By a vote of 81 to 18, the upper chamber approved the agreement which was negotiated by Senate Majority Leader Harry Reid, D-Nev., and Minority Leader Mitch McConnell, R-Ky. It will fund the government through Jan. 15 and lift the debt ceiling through Feb. 7.
"This compromise we reached will provide our economy with the stability it desperately needs," Reid said on the floor earlier Wednesday when he announced an agreement had been reached. "It's never easy for two sides to reach consensus. It's really hard, sometimes harder than others. This time was really hard."
Several of the Senate's most conservative members voted against the bill because they felt it did not do anything to dismantle the Affordable Care Act.
"This is a terrible deal," said Sen. Ted Cruz, R-Texas, on the Senate floor before the vote, though he acknowledged that it would pass. "This deal embodies everything about the Washington establishment that frustrates the American people."
In addition to funding the government and lifting the debt ceiling, the agreement authorizes retroactive pay for federal employees who were furloughed and instructs the government to reimburse states for the costs they incurred executing federal programs during the shutdown.
The House is expected to vote on the measure later Wednesday evening after Republicans spent Tuesday struggling - and failing - to put together their own deal that could pass the entire conference. It will take a combination of Republicans and Democrats to garner the necessary 217 votes.
"Blocking the bipartisan agreement reached today by the members of the Senate will not be a tactic for us. In addition to the risk of default, doing so would open the door for the Democratic majority in Washington to raise taxes again on the American people and undo the spending caps in the 2011 Budget Control Act without replacing them with better spending cuts," House Speaker John Boehner, R-Ohio, said in statement Wednesday afternoon. "Our drive to stop the train wreck that is the president's health care law will continue. We will rely on aggressive oversight that highlights the law's massive flaws and smart, targeted strikes that split the legislative coalition the president has relied upon to force his health care law on the American people."
When the deal was announced earlier in the day, McConnell similarly promised that Republicans "remain determined to repeal" Obamacare and would fight to ensure none of the mandatory spending cuts mandated by the sequester were overturned.
As part of the deal, congressional will name negotiators to a group, led by Sen. Patty Murray, D-Wash., and Rep. Paul Ryan, R-Wis., that is charged with crafting a larger, long-term budget deal due in December.
Though House Republicans have almost nothing in the bill that they can call a victory, they have not taken out their frustration on Boehner.
"I think Speaker Boehner has done a fantastic job the last two and a half weeks. I think he has listened to his conference," said Rep. Raul Labrador, R-Idaho, at a gathering of conservatives Wednesday morning. "I am more disappointed in some of the Republicans that have been wanting to cave from the beginning. Instead of giving the Speaker the ability to fight, they have been just continually going to the media and complaining about the fact that we are in a fight."
Several conservative groups urged lawmakers to vote against the bill. "The proposed deal will do nothing to stop Obamacare's massive new entitlements from taking root -- radically changing the nature of American health care," said one such group, Heritage Action.