In a twist, Murkowski said she will state her opposition but vote "present" as a courtesy to Kavanaugh supporter Sen.
The Alaskan senator's vote was the latest example of the independent streak she forged since overcoming a Republican primary challenge in 2010 to win re-election as a rare write-in candidate.
Friday's vote concerned issues that "are bigger than the nominee" and are necessary for fully functioning legislative and judicial branches, Murkowski said.
Republican Sen. Jeff Flake of Arizona also said on MSNBC on Friday he would vote yes on Kavanaugh's final confirmation barring no late breaking developments.
Murkowski broke with her party as the only one of four key swing votes to oppose advancing his nomination.
VERIFY: Everything to know about the Supreme Court confirmation process
During the rally, the president also accused Democrats of supporting sanctuary cities and of wanting to strip funding from U.S. Trump stepped into the political battle over the confirmation as allegations piled up against Kavanaugh.
Collins' decision leaves opponents of Kavanaugh hoping for an unlikely scenario of at least two other senators who had previously backed him to change their minds and declare they will vote against him.
White House and Republican Senate leaders said the Federal Bureau of Investigation report revealed no evidence of wrongdoing, while Democrats said the White House tied the FBI's hands and the probe is not thorough.
The president said at a rally in Minnesota on Thursday night that Democrats attempted to "destroy" his Supreme Court nominee and his supporters were moving up in a bid to keep Republican control of Congress in the November 6 midterm elections.
Sen. Charles Grassley, R-Iowa, told reporters that the Senate Judiciary Committee's inability to attract Republican women might be caused by its heavy workload, a remark the panel's chairman tried to retract a few minutes later. And that report might give her an excuse to vote for Kavanaugh.
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But it said a top-secret U.S. government investigation, dating from 2015 and involving the FBI, remains open. Amazon reported the discovery to USA authorities, sending a shudder through the intelligence community.
The vote occurred shortly before 4 p.m.
The Republicans appear to have the votes to confirm Judge Brett Kavanaugh to the Supreme Court, and the Senate's up-or-down vote will take place this afternoon.
US President Donald Trump nevertheless cheered the result of the cloture vote.
Republicans have a 51-49 majority in the Senate. Some wore shirts that said "Confirm Kavanaugh Now", and "I stand with Brett", while others had buttons that said, "Believe Survivors".
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All proceeds gathered at Tough Enough to Wear Pink will be donated to the American Cancer Society for its breast cancer programs. Bush said football coaches and players, cheer and pom will all sport pink to call attention to the threat of breast cancer.
They converged on Capitol Hill and held a rally outside the Supreme Court, chanting: "Kavanaugh has got to go!" Eventually, Flake voted to recommend Kavanaugh for confirmation but conditioned his final vote on the FBI conducting a seventh background investigation on Kavanaugh.