The action means a simple majority can approve presidential nominees, except for U.S. Supreme Court positions, instead of a 60-vote majority in the 100-member Senate to overcome filibustering senators.
"It's no secret that the American people have probably never been more frustrated with Washington," Obama told reporters. "And one of the reasons why that is, is that over the past five years, we've seen an unprecedented pattern of obstruction in Congress that's prevented too much of the American people's business from getting done. ...
"Now, at a time when millions of American have desperately searched for work, repeated abuse of these tactics have blocked legislation that might create jobs. They've defeated actions that would help women fighting for equal pay. They've prevented more progress than we would have liked for striving young immigrants trying to earn their citizenship. Or it's blocked efforts to end tax breaks for companies that are shipping jobs overseas."
Obama said it has harmed "our economy, and it's been harmful to our democracy. And it's brought us to the point where a simple majority vote no longer seems to be sufficient for anything, even routine business through what is supposed to be the world's greatest deliberative body."
The president conceded filibuster tactics had been developed by both parties over the years.
Republicans warned what goes around comes around, saying Democrats will "regret this" after Majority Leader Harry Reid invoked a change in Senate rules that stopped the filibusters.
The Senate voted 55-43 to end debate on the nomination of Patricia Millett, named by President Obama to a judgeship on the District of Columbia federal court, The Hill reported.
That was preceded by a 52-48 vote to remove a requirement for a 60-vote majority on nominations other than those to the U.S. Supreme Court. Three Democrats -- Carl Levin of Michigan, Mark Pryor of Arkansas and Joe Manchin of West Virginia -- joined all Republicans in voting against the change.
Republicans had blocked the nominations of Millett, Robert Wilkins and Cornelia Pillard. A fourth nominee, Caitlin Halligan, withdrew her name after Republicans threatened to block her confirmation.
The change -- sometimes referred to as the "nuclear option" because of its potential to destroy bipartisan cooperation in the chamber -- allows most presidential appointments to be ratified with a simple majority.
Senate Majority Leader Harry Reid, D-Nev., invoked the options after Republicans blocked votes on the three nominees to the D.C. Circuit Court of Appeals in the past month, Politico reported.
Friction caused by Reid's use of the "nuclear option" was evident in the vote. Sens. Lisa Murkowski, R-Alaska, and Susan Collins, R-Maine, had previously voted to approve Millet's nomination. Thursday, they voted against it.
"These nominees deserve at least an up or down vote, yes or no," Reid said in a speech on the Senate floor before the vote on changing the rule. "But Republican filibusters deny them a fair vote, any vote, and deny the president his team.
"It's time to change the Senate before this institution becomes obsolete," Reid said.
Minority Leader Mitch McConnell, R-Ky., accused Reid of starting a "fake fight" to distract from the controversy over the Affordable Care Act.
"You'll regret this and you might regret it even sooner than you might think," he warned Reid earlier in the morning.