The Senate's 54-44 vote Friday was strictly along party lines in favor of the bill, which would prevent a shutdown of nonessential government services.
That followed a 79-19 vote to cut off a filibuster by Sen. Ted Cruz, R-Texas, that exposed a rift among Republicans eager to prevent a shutdown and those, like Cruz, who seem willing to risk one over the health overhaul.
All 52 Democrats, two independents and 25 of 44 Republicans voted in favor. That included Minority Leader Mitch McConnell, R-Ky., and most of the GOP leadership.
Cruz was trying to rally House conservatives to continue the battle over heath care. He was urging them to reject efforts by Boehner and other GOP leaders to offer scaled-back assaults on the law such as repealing the tax on medical devices as the House response.
Some conservatives were taking their cues from Cruz rather than party leaders such as Boehner hoping to avoid a shutdown. Closing down the government could weaken Republicans heading into an even more important battle later in October over allowing the government to borrow more money.
If lawmakers miss the deadline, hundreds of thousands of nonessential federal workers would have to stay home on Tuesday.
Critical services such patrolling the borders, inspecting meat and controlling air traffic would continue. Social Security benefits would be sent and the Medicare and Medicaid health care programs for the elderly and poor would continue to pay doctors and hospitals.
The new health insurance exchanges would open Tuesday, a development that's lent urgency to the drive to use a normally routine stopgap spending bill to gut implementation of the law.
Associated Press writers Josh Lederman and David Espo contributed to this report.