Passage is expected next month for extending the law that was passed weeks after the Sept. 11, 2001, attacks as a weapon to help the government track terror suspects.
The 96-3 vote Thursday was no surprise to Sen. Russell Feingold, the Wisconsin Democrat who was the lone senator to oppose the law four and a half years ago and is the chief obstacle to extending 16 provisions now due to expire March 10.
Feingold, who is considering seeking his party's presidential nomination, plans to make the Senate spend several more days on the bill.
He complained that Majority Leader Bill Frist, R-Tenn., had used procedural maneuvers to prevent him from trying to add more protections for people investigated by the government.
"We still have not addressed some of the most significant problems with the Patriot Act," Feingold said.
At the White House, spokesman Scott McClellan urged the Senate to keep up the momentum on the legislation, which he called "a good faith effort" to improve the law.
"Yet there are still some Senate Democrats that want to continue to engage in obstructionist tactics and prevent this vital legislation from being reauthorized," McClellan said. "We hope the Senate will move ahead quickly and reject the continued obstructionist efforts."
Only Sens. Jim Jeffords, I-Vt., and Robert C. Byrd, D-W.Va., supported Feingold on Thursday's vote to stop what Frist had characterized as a filibuster preventing the Senate from acting on the legislation. Sen. David Vitter, R-La., did not vote.
The changes Feingold was seeking included an amendment that would set a four-year expiration date on Patriot Act provisions regarding National Security Letters — demands made to banks, libraries, Internet providers and others without warrants — for records of their customers or clients.
Another amendment would require the government to notify the subject of a secret search within seven days or obtain court permission to maintain the secrecy for a longer period.