Invoking the long-threatened “nuclear option” means that most of President Barack Obama’s judicial and executive branch nominees no longer need to clear a 60-vote threshold to reach the Senate floor and get an up-or-down vote.

Speaking at the White House, Obama praised the Senate action, accusing Republicans of attempting to block his nominees based on politics alone, not on the merits of the nominee.

“This isn’t obstruction on substance, on qualifications. It’s just to gum up the works,” he said.

( PHOTOS: Harry Reid’s career)

Senate Majority Leader Harry Reid (D-Nev.) used the nuclear option Thursday morning, meaning he called for a vote to change the Senate rules by a simple majority vote. It passed, 52 to 48. Three Democrats voted against changing the rules — Sen. Carl Levin of Michigan, Joe Manchin of West Virginia and Mark Pryor of Arkansas.

“It’s time to change the Senate before this institution becomes obsolete,” Reid said in a lengthy floor speech on Thursday morning.

A furious Senate Minority Leader Mitch McConnell (R-Ky.), who tried to recess the Senate for the day before the rules change could get a vote, said after the minority’s power was limited by Democrats: “I don’t think this is a time to be talking about reprisal. I think it’s a time to be sad about what has been done to the United States Senate.”

But McConnell quickly noted that Republicans could fix the problem in the upcoming midterm elections if they regain the majority: “The solution to this problem is an election. The solution to this problem is at the ballot box. We look forward to having a great election on 2014.”

The debate over the filibuster — and specifically its use on D.C. Circuit nominees — has been raging for nearly a decade, stretching back to when George W. Bush was president and Democrats were in the minority. But changing the Senate rules has always been avoided through a piecemeal deal, a gentleman’s agreement or a specific solution, not a historic change to the very fabric of the Senate.

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But since Obama’s nomination, the “nuclear option” has reared its head three times in less than a year — each time getting closer to the edge. Many in the Senate privately expected that this go-round would be yet another example of saber rattling, but Reid said pressure was increasing within his own party to change the rules.

The blockade of three consecutive nominees to a powerful appellate court was too much for Democrats to handle — and Reid felt compelled to pull the trigger, explaining that “this is the way it has to be.”

It didn’t take long for Republicans to begin circulating both Reid’s and Obama’s past statements opposing a rules change. But the majority leader said that things escalated to a level that even he had not thought possible in 2005, when a “Gang of 14” banded together to stop a rules change.

“They have done everything they can to deny the fact that Obama has been elected and then reelected,” he said. “I have a right to change how I feel about things.”

( Earlier on POLITICO: Court nominees: Battleground for partisan politics)

Senate Democrats were quick to use their newfound powers, voting in the early afternoon to end the filibuster on Patricia Millett’s nomination to the D.C. Circuit Court of Appeals. The vote was 55-43, with two senators voting present. Before the change earlier Thursday, Millett would have needed 60 votes to clear the procedural hurdle and move on to a confirmation vote. But now, she needed just 51 to advance.

In his speech, Obama noted that in the few decades before he took office, about 20 nominees were filibustered. Since he took office, close to 30 judicial and political nominees have had their nominations blocked.

“It’s no secret that the American people have probably never been more frustrated with Washington, 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,” Obama said. “Today’s pattern of obstruction just isn’t normal. We can’t allow it to become normal.”

Obama also cited the filibuster of a gun control bill earlier this year, although Thursday’s rule change would preserve the filibuster for Supreme Court picks and legislation.

The Senate’s vote to push the button on the “nuclear option” is unprecedented and is likely to lead to a further erosion of the filibuster in the future. But for now, Senate Democrats haven’t pursued eliminating the filibuster on lawmaking, partially because Republicans control the House and frequently choose not to take up Senate-passed bills anyway.

Underscoring the historic nature of Reid’s action, nearly all 100 senators were seated at their desks in the chamber — a rare sight, particularly when the Senate opens in the morning for business.

McConnell was quick to criticize Reid’s plan, accusing Democrats of trying to divert attention from the embattled health care law that has been a drag on the party. McConnell said Democrats were cooking up a “fake fight over judges that aren’t even needed.”

“You’ll regret this and you might regret it even sooner than you might think,” McConnell warned.

And on the other end of the Capitol, Speaker John Boehner (R-Ohio) charged that Reid is trying to distract the public away from the rollout of the Affordable Care Act.

“Sounds to me like Harry Reid is trying to change the subject,” he told reporters at his weekly news conference.“If I were taking all the incoming fire that he’s taken over Obamacare, I’d try to change the subject, too.”

Privately, Senate Democratic leaders insist they preferred confirmation of Obama’s nominees rather than a rules change. And lawmakers have been at this point before. But increasingly even longtime protectors of the Senate’s rules have been changing their tune, including Vice President Joe Biden, who said he supported Reid’s effort on Thursday morning.

The Senate’s new rules will also pave the path toward smoother confirmation for two more key Obama nominees: Janet Yellen to lead the Federal Reserve and Jeh Johnson to helm the Department of Homeland Security. Another nominee blocked by Republicans, Rep. Mel Watt’s pick to helm the Federal Housing Finance Agency, will likely benefit.

Republicans are publicly warning that the change would simply be a path to eliminating the filibuster on everything, even on legislation — which would mean when the GOP takes the majority, Democrats will regret pushing the nuke button.

“You always have to take it seriously. I just think it would be incredibly short-sighted,” said Sen. John Cornyn of Texas, the Republican whip. “It just seems to be something they keep coming back to when [Democrats] don’t get their way.”

The Senate came to the brink of a more narrow rules change that would have affected only executive nominees this summer but longtime lawmakers like Sens. John McCain (R-Ariz.) and Lindsey Graham (R-S.C.) were able to agree to help move a series of stalled nominations and avoid diluting the minority’s power.

This time around there hasn’t been as strong an effort to head off the rules change. McCain made an offer on Wednesday that Democrats found insufficient because it didn’t include all three judges; Reid has long said he won’t settle for less than filling out the 11-seat court’s three vacancies.

But not all Democrats have been wedded to a rules change, and some worked proactively to figure out if the “nuclear option” could be avoided. For instance, Pryor helped avoid the “nuclear option” in 2005 when Republicans were trying to change the rules to circumvent Democratic filibusters of George W. Bush’s judicial nominees and again tried to find a solution this time around.

Facing a difficult reelection bid next year, Pryor voted against the sweeping change on Thursday and quickly sought to distance himself from his party.

“Today’s use of the ‘nuclear option’ could permanently damage the Senate and have negative ramifications for the American people,” Pryor said. “This institution was designed to protect — not stamp out — the voices of the minority.”

In addition to Wilkins, Pillard and Millett, Republicans also blocked the elevation of Watt and a fourth D.C. Circuit nominee in March, Caitlin Halligan. A fifth nominee, Sri Srinivasan, was confirmed to the court unanimously in May.

Manu Raju and Jennifer Epstein contributed to this report.