The potentially controversial nominations come as Obama begins to shape his national security team for his second term.
The nominations of Hagel and Brennan must be confirmed by the US Senate.
Hagel, a former Republican senator who would replace the retiring Leon Panetta as head of the Pentagon, has faced criticism over the depth of his commitment to Israel's security. But the Vietnam War veteran has also received support from prominent US military leaders.
Hagel was accused of making anti-Semitic comments in 2007 after using the term "Jewish lobby" to describe pro-Israel advocacy groups that he said "intimidate" Washington lawmakers.
The former senator also drew criticism over comments he made in 1998 after opposing the nomination of a potential US ambassador that he described as "openly, aggressively gay".
Hagel has since apologised for the statement.
In announcing the nomination at the White House Monday, Obama said Hagel would be the first person of enlisted rank and the first Vietnam War veteran to serve as secretary of defense.
Obama called Hagel "the leader that our troops deserve".
If confirmed, Brennan would succeed retired Army Gen. David Petraeus as head of the CIA.
Petraeus resigned earlier this year after admitting to an extramarital affair with his biographer, Paula Broadwell.
Obama described Brennan as "tireless", and said he would remain "relentless" in pursuit of Al Qaeda.
Brennan was nominated for the post in 2008 but withdrew himself from consideration after he faced questions regarding his views on so-called "enhanced interrogation" techniques, such as waterboarding, used on terrorism suspects under the administration of president George W. Bush.
Many of the interrogation techniques are widely considered torture, and Brennan has said he opposes the waterboarding. But he said in 2007 that such tactics did produce actionable intelligence from "real hardcore terrorists".
Brennan's latest nomination is widely expected to go much more smoothly.
"The issue has been removed from the debate because the president and John Brennan, as his top counterterrorism adviser, brought those techniques to an end," Ben Rhodes, Obama's deputy national security adviser, told CBS News.