Sen. Claire McCaskill, D-Mo., questioned how the confirmation process devolved into a character assassination in which Hagel was accused of "having secret ties with our enemies."
"I sincerely hope that the practice of challenging nominations with innuendo and inference, rather than facts and figures, was an aberration and not a roadmap," she said in a statement after the vote.
Obama got no points with the GOP for tapping the former two-term Republican senator. GOP lawmakers excoriated Hagel and cast him as a radical far out of the mainstream.
Sen. John McCain, R-Ariz., clashed with his onetime friend over his opposition to President George W. Bush's decision to send an extra 30,000 troops to Iraq in 2007 at a point when the war seemed in danger of being lost. Hagel, who voted to authorize military force in Iraq, later opposed the conflict, comparing it to Vietnam and arguing that it shifted the focus from Afghanistan.
McCain said several GOP lawmakers also had "a lot of ill will" toward the moderate Republican for his criticism of Bush and his backing for Democratic candidates.
Shortly after a White House meeting with Obama on immigration on Tuesday, McCain voted against his onetime friend and fellow Vietnam veteran.
Republicans also challenged Hagel about a May 2012 study that he co-authored for the advocacy group Global Zero, which called for an 80 percent reduction of U.S. nuclear weapons and the eventual elimination of all the world's nuclear arms.
In an echo of the 2012 presidential campaign, Hagel faced an onslaught of criticism by well-funded, Republican-leaning outside groups that labeled the former senator "anti-Israel" and pressured senators to oppose the nomination. The groups ran television and print ads criticizing Hagel.
Opponents were particularly incensed by Hagel's use of the term "Jewish lobby" to refer to pro-Israel groups. He apologized, saying he should have used another term and should not have said those groups have intimidated members of the Senate into favoring actions contrary to U.S. interests.