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* Just four Republicans join Democrats to back Hagel
* Confirmation ends unusually long and bitter nomination fight
* Fight may have weakened Hagel before difficult job at Pentagon (Adds quotes, comments, background.)
By Patricia Zengerle
WASHINGTON, Feb 26 (Reuters) - The U.S. Senate confirmed Chuck Hagel as President Barack Obama's new secretary of defense on Tuesday, after an unusually acrimonious confirmation fight that threatened to complicate his work as civilian leader at the Pentagon.
The Senate voted 58-41 to confirm the former Republican senator, the closest vote ever to approve a defense secretary.
Just four Republicans - Mike Johanns of Nebraska, who holds Hagel's old Senate seat, Thad Cochran of Mississippi, Richard Shelby of Alabama and Rand Paul of Kentucky - joined the Democrats and independents in support of Hagel's nomination.
After the hard-fought victory, the Democratic president said he was pleased there had been bipartisan support for Hagel, a decorated veteran who served during the Vietnam War as an enlisted man before becoming a Republican U.S. senator.
"I am grateful to Chuck for reminding us that when it comes to our national defense, we are not Democrats or Republicans, we are Americans, and our greatest responsibility is the security of the American people," Obama said.
The bruising battle over Hagel was one of many bitter partisan struggles between Democrats and Republicans at a time when Congress is widely criticized for its inability to agree on even the most basic measures to run the country.
The Senate had voted earlier on Tuesday to end debate on Hagel and move forward, almost two weeks after Republicans launched a filibuster to block the nomination. It was the first ever used to delay consideration of a defense nominee, prompting Democrats to accuse Republicans of jeopardizing national security.
Republicans have also challenged Obama's choice to be CIA director, John Brennan, although that nomination appears to be on track, with a vote by the Senate Intelligence Committee expected on Thursday.
In a sign that opposition to Obama's nominations could be easing, the Senate Finance Committee on Tuesday backed his nominee to lead the U.S. Treasury, Jack Lew, with the support of about half the panel's Republicans.
BUDGET, IRAN, ISRAEL AMONG CONCERNS
Hagel had angered party leaders as a senator when he criticized former President George W. Bush's handling of the Iraq war.
Many Republicans opposed to Hagel's nomination raised questions about whether he is sufficiently supportive of Israel, tough enough on Iran or truly committed to maintaining a robust nuclear deterrent.
After Hagel's shaky performance during his confirmation hearing before the Senate Armed Services Committee, opponents questioned whether he was capable of running the vast Pentagon bureaucracy. Some feared he would be too complicit in efforts by Obama to cut Pentagon spending as a way to deal with yawning U.S. budget deficits.
Some defense industry executives worried that Hagel would be hamstrung from the start, saying his difficult confirmation could severely limit his ability to negotiate with Congress.
"They've neutered him already," said one industry executive, who was not authorized to speak publicly.
Although the Senate rejected John Tower as President George Bush's Pentagon pick in 1989 by a 53-47 vote, defense nominees are typically confirmed by large margins. Leon Panetta, whom Hagel replaces as defense secretary, was approved by a unanimous vote of 100 to nothing in June 2011.
But political experts said such concerns were overblown, given the vast partisan divide that already exists between the Democratic White House and Republicans in Congress on most issues.
"The confirmation process probably leaves a few light scars on Hagel because Republican critics have raised doubts about his judgment," said Sarah Binder, a congressional expert at the Brookings Institution.
"But I think Hagel would have faced tough scrutiny and criticism from Republicans once in office, even had he originally sailed to confirmation," she said.
Hagel said he was honored to return to public service. "I will work closely with Congress to ensure that we maintain the strongest military in the world and continue to protect this great nation," he said in a statement.
Hagel will be sworn in on Wednesday morning.
SEQUESTRATION CUTS LOOM OVER PENTAGON
Hagel's confirmation comes as the Pentagon faces the prospect of cutting $46 billion in spending over the next seven months of the fiscal year. The cut, scheduled to go into effect on Friday, comes as the department is already implementing $487 billion in spending reductions over the next decade.
Some of Hagel's most vehement opponents made a last-ditch appeal to stop the nomination before the vote.
James Inhofe, the senior Republican on the Senate Armed Services Committee, said he had even called Panetta and asked him not to retire. Panetta, 74, who has made no secret of his desire to be home in California, declined.
After the vote, Inhofe said he still had "serious concerns" about Hagel's ability to lead the Department of Defense but was "ready and willing" to work with him. He urged Hagel to make his first order of business averting the looming defense cuts. (Additional reporting by Richard Cowan, David Alexander, Andrea Shalal-Esa, Phil Stewart and Matt Spetalnick; Editing By Doina Chiacu)