"I do not believe that Chuck Hagel, who is a friend of mine, is qualified to be secretary of defense, but I do believe that elections have consequences -- unfortunately," McCain told CNN's Candy Crowley Sunday on "State of the Union," explaining why he chose not to sign. "And the president of the United States was re-elected."
Obama announced his support for Hagel two weeks before the kick-off of his second term.
Hagel is a former GOP senator from Nebraska and Purple-Heart-decorated Vietnam veteran.His confirmation today makes him the first former enlisted member of the Armed Forces to serve as secretary of defense, but he has been an unpopular pick from the start, with groups claiming he was anti-Israel and anti-gay rights.
The hearings over Hagel's nomination have had tense moments, with many serious accusations and at least one bordering on the bizarre.
Republicans have raised questions about Hagel's finances. A letter signed by 20 senators faulted Hagel for failing to disclose information about compensation he and organizations he worked with received during the last decade.
McCain also accused Hagel of being on "the wrong side of" history for his opposition to President Bush's 2007 surge of American troops in Iraq.
A conservative website attacked Hagel for taking money from a group called "Friends of Hamas," which was later revealed to be an imaginary entity dreamed up by New York Daily News reporter Dan Friedman.
Hagel takes the place of departing Defense Secretary Leon Panetta.
In his farewell message, Panetta called leading the Defense Department "the privilege of my life," and said he's most proud of the progress made in ending the wars in Iraq and Afghanistan, success in weakening al Qaeda and developing a defense strategy based on "fiscal discipline." In a nod to ending "don't ask, don't tell" and the ban on women in combat, Panetta also said he was proud that in his tenure the Pentagon expanded "opportunities for everyone in the military, because I believe everyone deserves a chance to serve."
ABC's Dana Hughes contributed to this report.