The vote was 51-46, with six Democrats joining most Republicans in supporting Holmes. Five Republicans opposed him.
President Bush nominated Holmes, 53, for the U.S. District Court in the Eastern District of Arkansas in January 2003, but the nomination was slowed as attention turned to some of Holmes' writings on his Catholic faith and rape victims.
He apologized for writing in 1980 that rape victims rarely get pregnant, calling them a "red herring" in the debate over abortion. But Holmes said his 1997 comparison of the Catholic Church's subservient relationship with Jesus Christ to a wife's duties to her husband was unfairly taken out of context. In an article he co-authored with his wife, he said a wife has an obligation "to subordinate herself to her husband" and "to place herself under the authority of the man."
Sen. Kay Bailey Hutchison, R-Texas, cast her first vote against a Bush nominee when she opposed Holmes. "He doesn't have the fundamental commitment to the total equality of women in our society," she said in explaining her vote.
Several women's and liberal advocacy groups said Holmes' strident opposition to abortion makes him unfit to serve as a federal judge.
But Sen. Blanche Lincoln, D-Ark., said Holmes has the right to express his religious views, noting his stated remorse over his rape remark. "I, for one, accept his apology," Lincoln said.
Some supporters contended anti-Catholic bias was at work in the opposition to Holmes, a charge Republicans first raised when the Senate was considering the nomination of former Alabama Attorney General William Pryor (search) as an appeals court judge.
Sen. Jeff Sessions said members of other faiths would never be subjected to the treatment accorded Holmes. "Are we going to demand that they come before the Senate Judiciary Committee and renounce their faith before they become a federal judge?" Sessions said.
Bush gave Pryor a recess appointment in February, breaking the Democrats' hold on the nomination.
Holmes, interviewed after the vote, said he would have withdrawn his nomination if Lincoln or Arkansas's other senator, Democrat Mark Pryor, had opposed him. And he acknowledged that election year politics might have factored into the Senate's consideration.
"I recognize that people differ on nominations and any time you go into a political process like this there's potential for political concerns to play a part in the disposition of the issue," Holmes said.
He was the last of 25 judicial nominees the Senate voted on as part of an agreement struck by Bush and Senate Democrats in May. The deal guaranteed the Senate would vote on 25 mainly uncontroversial nominees if the president agreed to stop using recess appointments to install his most contentious nominees on federal appeals courts while Congress is out of town.
The others were confirmed with ease before Congress' July 4 recess.
Holmes' nomination advanced from the Senate Judiciary Committee a year ago. But in an unusual move, the committee sent the nomination to the full Senate without a recommendation.