Holder went further, telling the CIA that the government would provide free legal representation to its employees in any legal proceeding or congressional investigation related to the program, and would repay any financial judgment.
"It would be unfair to prosecute dedicated men and women working to protect America for conduct that was sanctioned in advance by the Justice Department," Holder said.
Obama said in his statement and a separate letter sent directly to CIA employees that the nation must protect their identity "as vigilantly as they protect our security."
Current CIA Director Leon Panetta said in a message to his employees: "CIA responded, as duty requires."
Panetta had been among those seeking to have more of the memos blacked out, according to a government official who declined to be identified because he was not authorized to release the information.
The CIA has acknowledged using waterboarding on three high-level terror detainees in 2002 and 2003, with the authorization of the White House and the Justice Department. Hayden said waterboarding has not been used since, but some human rights groups have urged Obama to hold CIA employees accountable for what they, and many Obama officials, say was torture.
The memos produced by the Justice Department's Office of Legal Counsel were released to meet a court-approved deadline in a lawsuit against the government in New York by the American Civil Liberties Union.
"It's impossible not to be shocked by the contents of these memos," ACLU lawyer Jameel Jaffer said. "The memos should never have been written, but we're pleased the new administration has made them public."
Associated Press writer Pamela Hess contributed to this report.