The provision, part of a broad intelligence authorization bill passed by the House and Senate, would prohibit any interrogation techniques to be used on prisoners that are not authorized or condoned by the U.S. Army Field Manual.
CBS News White House Correspondent Mark Knoller reports that the White House is confident that the president's veto would be sustained.
The bill passed the Senate by a vote of 51 to 45; 5 Republicans joined 45 Democrats and 1 independent in favor of the ban.
White House press secretary Dana Perino characterized the confrontation in partisan terms, saying Americans will have to choose between supporting a ban on waterboarding and protecting national security: "They'll have to ask themselves, 'Do you trust the intelligence community more than you trust Democrats who are beholden to their left wing?' And that's the debate that this country is going to have."
Sen. John McCain, who has previously spoken out against torture (having been tortured himself while held captive during the Vietnam War), voted against the bill, but said his vote was not inconsistent with his previous calls for a ban.
McCain had earlier sponsored the 2006 Detainee Treatment Act which included a ban on waterboarding, which President Bush invalidated by a signing statement giving himself the authority to ignore it.
"What we need is not to tie the CIA to the Army Field Manual, but rather to have a good faith interpretation of the statutes that guide what is permissible in the CIA program," McCain said, in stating his opposition to the bill.
"We're now at the point where we have a clear and concrete law," said Sen. Charles Schumer, D-N.Y. "It's up to the president to sign the bill. If the president vetoes the intelligence authorization, he will be voting in favor of waterboarding, plain and simple - no ands, ifs or buts."
Schumer also warned that a presidential veto of the authorization bill "will hamstring our ability to gather and act on important intelligence at a time of war."
The administration's view is that the ban on waterboarding would force the CIA to shut down its program of enhanced interrogation of terror suspects, something President Bush regards as an important tool in the war on terror.
Although President Bush has stated that the United States has not and will not torture people, it has been learned that Mr. Bush himself has authorized the use of waterboarding on detainees (a practice previously prosecuted by the United States as a war crime), and has claimed the authority to do so again in certain circumstances.
Despite military interrogators' assertions that waterboarding and other brands of torture do not produce reliable intelligence, the Bush administration continues to argue that it needs the option of waterboarding when seeking information from recalcitrant prisoners.
Attorney General Mike Mukasey has declined to declare that waterboarding is torture, despite congressional demands during and after his Senate confirmation process, fueling the administration critics' assumption that admitting such would expose administration figures who authorized the practice to criminal prosecution.
Despite the fight over the waterboarding ban, a senior U.S. Justice Department official said Thursday that laws and other limits enacted since three terrorism suspects held by the CIA were waterboarded have eliminated the technique from what is now legally allowed by the Agency.
"The set of interrogation methods authorized for current use is narrower than before, and it does not today include waterboarding," Steven G. Bradbury, acting head of the Justice Department's Office of Legal Counsel, says in remarks prepared for his appearance Thursday before the House Judiciary Constitution subcommittee.
"There has been no determination by the Justice Department that the use of waterboarding, under any circumstances, would be lawful under current law," he said, avoiding suggestion that waterboarding might be considered legal in the future.
In 2005 Bradbury signed two secret legal memos authorizing the CIA to use waterboarding, as well as physical violence and freezing temperatures, when questioning terror detainees. Because of those opinions, Senate Democrats have opposed his nomination to formally head the legal counsel's office.
Judge Dismisses Detainee Rendition Lawsuit
In a related story, a federal judge on Wednesday threw out a lawsuit accusing a subsidiary of Boeing Co. of illegally aiding the CIA's secret rendition program by flying detainees overseas where they could be tortured.
U.S. District Court Judge James Ware accepted the arguments made by CIA Director Gen. Michael Hayden, who had earlier evoked the "state secrets privilege," saying that going forward with the case would jeopardize national security.
The American Civil Liberties Union lawsuit was filed against Jeppesen Dataplan Inc., of San Jose, Calif.
In arguments Tuesday, ACLU lawyers had said that many of the facts about the rendition program were already public knowledge.
CBSNews.com producer David Morgan contributed to this report.