The 52-48 vote to undercut venerable filibuster rules on presidential appointees capped more than a decade of struggle in which presidents of both parties complained about delays in confirming appointees, particularly to the federal courts.
Senate Majority Leader Harry Reid, who launched the move, accused Republicans of "unbelievable, unprecedented obstruction" of Obama's selections to fill court vacancies and other offices.
"It's time to change the Senate, before this institution becomes obsolete," he said.
His Republican counterpart, Sen. Mitch McConnell of Kentucky, accused Democrats of exercising raw power and said they would regret it when political fortunes switched.
He likened the effort to the president's since-discredited promise that Americans who like their health care can keep it under "Obamacare," noting that Reid promised last summer he wouldn't seek to change the process for approving appointees. "He may as well just have said, 'If you like the rules of the Senate, you can keep them,'" McConnell said.
At issue was a rule that can require a 60-vote majority to assure a yes-or-no vote on presidential nominees to the courts or to Cabinet departments or other agencies.
Under a parliamentary maneuver scripted in advance, Democrats led by Reid sought to change proceedings so that only a simple majority was required to clear the way for a final vote.
Supreme Court nominations would be exempted from the change and subject to a traditional filibuster, the term used to describe the 60-vote requirement to limit debate.
The move was backed by all but three Democrats and opposed by all the Senate's Republicans. Democratic dissidents were Sens. Carl Levin of Michigan, Joe Manchin of West Virginia and Mark Pryor of Arkansas.
Pryor issued a statement saying the Senate "was designed to protect_not stamp out_the voices of the minority."
The change is the most far-reaching since 1975, when a two-thirds requirement for cutting off filibusters against legislation and all nominations was lowered to 60 votes.
It would deliver a major blow to the GOP's ability to thwart Obama in making appointments, though Republicans have promised the same fate would await Democrats whenever the GOP recaptures the White House and Senate control.
It also could adversely affect the level of bipartisan cooperation in the Senate - a quality already in short supply in an era of divided government.
The maneuvering occurred after a decade in which first one party, then the other, nursed a lengthening list of grievances over delays in confirmation for nominees to the courts.
McConnell noted that Democrats sought to thwart some of President George W. Bush's conservative appointees, while Democrats say the GOP has done the same to Obama's appointees.
In a sign that a showdown was imminent, dozens of senators filed in to listen to Reid and McConnell swap accusations and then cast votes on a complicated series of parliamentary moves.
Even so, there was no doubt about the outcome, if Reid insisted. Democrats control 55 seats, compared with 45 for Republicans.
"These nominees deserve at least an up-or-down vote. But Republican filibusters deny them a fair vote," he said.
To which McConnell noted that the Senate has confirmed 215 of Obama's picks to the courts since he became president, and rejected two. "That's a confirmation rate of 99 percent," he said pointedly.
The nominee involved was Patricia Millett, an attorney and one of three nominees to the District of Columbia Circuit Court of Appeals whose nomination Republicans have prevented from coming to a final vote.
Few if any complaints have been lodged against the qualifications possessed by Millett or the other two appointees, District Judge Robert L. Wilkins and law professor Cornelia Pillard. Instead, Republicans have argued that there is no need to confirm any of the three because the court's caseload doesn't warrant it.
"The need for change is obvious," Reid, of Nevada, said in remarks on the Senate floor. He said that in the nation's history, there have been 168 filibusters against presidential appointees. "Half of them have occurred during the Obama administration - during the last four and a half years," he added.
Noting that Democrats have periodically talked of changing the rules in recent month, he added, "we're not interested in having a gun put to our head any longer."
It was unclear how quickly Millett might be confirmed.
The clash capped a period of increasing irritation on the part of Democrats.
"They have decided that their base demands a permanent campaign against the president and maximum use of every tool available," Sen. Jeff Merkley, D-Ore., a leading advocate of revamping filibuster rules, said Wednesday of Republicans. He said that consideration "is trumping the appropriate exercise of advice and consent" by GOP senators.
The D.C. Circuit Court is viewed as second only to the Supreme Court in power because it rules on disputes over White House and federal agency actions. The circuit's eight judges are divided evenly between Democratic and Republican presidential appointees.
Senior Democrats wary of future GOP retaliation until recently opposed the move, but growing numbers of them have begun lining up behind Reid's effort.
In addition, two dozen groups, including the AFL-CIO and Sierra Club, wrote lawmakers Wednesday supporting the change, saying that "rampant, ideology-based obstructionism is the new norm in the U.S. Senate."
Last summer, Democrats dropped threats to rewrite Senate rules after Republicans agreed to supply enough votes to end filibusters against Obama's nominees to the National Labor Relations Board as well as nominees to head the Environmental Protection Agency, the Labor Department and other agencies.