Ten Republicans voted for the spending bill, which passed 62-30, but one Democrat, Sen. Joe Manchin of West Virginia, joined the opposition to the resolution, The Hill reported.
The bill goes to President Barack Obama, who is expected to sign it, The Hill said. Without the resolution, the federal government would have been forced to shut down at the end of the month.
During debate on the bill Thursday, Manchin said "these continuing resolutions are suppose to be temporary, but it looks like they've become a permanent way of doing business."
Sen. Susan Collins, R-Maine, expressed similar sentiments.
"Rather than consider these appropriations bills, they'd rather kick the can down the road and pass a six-month extension," she said Wednesday.
Voting on the resolution was finally made possible after the chamber agreed to bring to a vote a bill by Sen. Rand Paul, R-Ky., to end aid to Egypt, Libya, Pakistan and Yemen unless they met certain conditions.
Paul had conducted a filibuster for several days to get the Senate to consider the bill. It was defeated 10-81.
The Senate voted 90-1 to approve a resolution introduced by Sen. Lindsey Graham, R-S.C., that the United States has a vital interest in working with other countries to prevent Iran from acquiring the capability for nuclear weapons.
Paul voted against the resolution, saying it was "a vote for pre-emptive war" against Iran.