WASHINGTON—The Justice Department said Thursday it won't bring charges in the deaths of two prisoners who allegedly were interrogated by the Central Intelligence Agency, closing a chapter in a nearly decade-old debate about the CIA's counterterrorism programs.

The department had already dropped most of the cases stemming from accusations that the CIA and other agencies committed abuses against detainees held by the U.S. after the Sept. 11, 2001, terrorist attacks. But Attorney General Eric Holder last year ordered a criminal...