The president, who endorsed the Senate and House bills, said he would be deeply involved in trying to help the two chambers work out their differences. But it is unclear how specific he will be  if, for example, he will push for one type of tax over another or try to concoct a compromise on insurance coverage for abortion.

Senator Olympia J. Snowe of Maine, a moderate Republican who has spent years working with Democrats on health care and other issues, said she was “extremely disappointed” with the bill’s evolution in recent weeks. After Senate Democrats locked up 60 votes within their caucus, she said, “there was zero opportunity to amend the bill or modify it, and Democrats had no incentive to reach across the aisle.”

Like many Republicans, Ms. Snowe was troubled by new taxes and fees in the bill, which she said could have “a dampening effect on job creation and job preservation.” The bill would increase the Medicare payroll tax on high-income people and levy a new excise tax on high-premium insurance policies, as one way to control costs.

When the roll was called Thursday morning, the mood was solemn as senators called out “aye” or “no.” Senator Robert C. Byrd, the 92-year-old Democrat from West Virginia, deviated slightly from the protocol.

Image Vice President Joseph R. Biden Jr. arrived for the vote at the U.S. Capitol on Thursday. Credit... Win McNamee/Getty Images

“This is for my friend Ted Kennedy,” Mr. Byrd said. “Aye!”

Senator Kennedy of Massachusetts, a longtime champion of universal health care, died of brain cancer in August at age 77.

Senator Jim Bunning, Republican of Kentucky, did not vote.

The fight on Capitol Hill prefigures a larger political battle that is likely to play out in the elections of 2010 and 2012, as Democrats try to persuade a skeptical public of the bill’s merits, while Republicans warn that it will drive up costs for those who already have insurance.