Sen. John McCain, R-Ariz., had battled with Johnson at confirmation hearing last month.
The Department of Homeland Security has a new Secretary Monday, after the Senate voted 78 to 16 to confirm Jeh Johnson.
The vote on the former Pentagon lawyer marks the end of widely expected confirmation, which was made almost inevitable by Majority Leader Harry Reid's decision to go nuclear last month.
Minority Leader Mitch McConnell, R-Ky., railed against the decision before the Senate took up a slate of nominees. The Kentucky Republican called it a "grave mistake" and tied it to what he believes is a larger narrative of the Obama administration and Democrats not playing by the rules.
"This vote isn't about any one nominee… It's about an attitude on the left that says the ends justify the means," he said, before the Senate voted on the first nomination.
Johnson received bipartisan support, though possible holds by Republican Sens. John McCain of Arizona, and Lindsey Graham of South Carolina, at times threatened his path to confirmation. Graham's hold wasn't specific to Johnson but against all nominees in an attempt to get survivors of the Benghazi terrorist attack to testify before members of Congress.
McCain battled with Johnson during his confirmation hearing last month over a request for information on border security. The Arizona Republican told the Associated Press that the nominee "refused to tell me that he would give me the information as to what is necessary to have 90 percent effective control of our border."
But Johnson was passed out of the Senate Homeland Security and Governmental Affairs Committee by a voice vote, with McCain and Sen. Rand Paul, R-Ky., being added to the record as no votes.
He received bipartisan praise during the committee's vote, with Sen. Tom Coburn, the committee's ranking member, noting that while he thinks the Homeland Security Department is dysfunctional, he considers Johnson an "open and honest broker."
Johnson is taking over an agency with a wide array of at times disjointed missions that has had to deal with low morale and holes in its leadership team.
He previously worked in the Pentagon helping develop some of country's top counterterrorism policies. He is replacing Janet Napolitano, who stepped down in September to become the first female president of the University of California. Rand Beers has stepped in as the acting secretary since then.
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