Hayden, 61, who has served as principal deputy to the US intelligence chief John Negroponte up to now, replaces Porter Goss, who was forced to resign earlier this month.
The 78-15 vote to confirm Hayden on Friday included the support of several Democrats in the Senate.
George Bush, the US president, who nominated Hayden as his candidate of choice, and the Senate were eager to get him confirmed before leaving on a week-long recess so that the top CIA job would not be vacant.
Goss resigned after clashing with Negroponte amid widespread concern about the future of the storied spy agency.
Reputation to restore
The CIA has seen its reputation eroded by reforms and intelligence breakdowns over the September 11, 2003 attacks and pre-war Iraq.
Dissenting votes came from Democrats who expressed concern over the National Security Agency spying programme that monitors the international phone calls and e-mails of US citizens without warrants while pursuing al-Qaeda suspects.
Hayden was NSA director when Bush ordered the programme in the aftermath of the September 11 attacks on Washington and New York.
Critics say the spying programme exceeds the president's constitutional powers and violates a federal law requiring court warrants for eavesdropping inside the United States.