The bill would ban what critics call "partial-birth" abortions, and Republican leaders hope to have the legislation on President Bush's desk by the end of next month.
Final passage is not in doubt, since the measure cleared the House and Senate by wide margins earlier this year.
The only difference between the two measures is a Senate-passed endorsement of the Supreme Court's 1973 ruling that declared women have the right to an abortion.
Republicans, who control the majority in both houses of Congress, plan to omit that provision from the final compromise.
But first, Sen. Barbara Boxer, a California Democrat who supports abortion rights, insisted on a separate vote on the issue.
"The majority of the people support" the court's landmark ruling, she said. "In my particular state, it is overwhelming."
But if Boxer wanted to turn the vote into a test of the merits of abortion rights, Republican supporters of the bill were eager to drain it of all practical significance.
Sen. Rick Santorum, R-Pa., a leading supporter of the bill, sharply challenged Boxer's assertion about widespread public support for the court ruling. At the same time, he said Wednesday's vote was a "routine vote that simply" advances the bill one step closer to final passage.
Mr. Bush has repeatedly urged Congress to enact the legislation. For their part, abortion rights supporters are ready to file suit in court attacking the measure as unconstitutional and vow the issue will finally be settled by the Supreme Court.
Under the bill, "partial-birth" abortion is defined as a procedure in which the fetus is killed after the entire fetal head is outside the body of the mother or, in the case of breech presentation, "any part of the fetal trunk past the navel is outside the body of the mother."
It does not apply to cases where the abortion is considered necessary because the life of the mother is at risk from some "physical disorder, physical illness, or physical injury."
Women cannot be imprisoned under the law, but doctors who violate the ban can be fined or jailed for up to two years. Doctors can also be sued by the fetus' father — if he is married to the mother — or by the woman's family if she is a minor. A physician accused of violating the law would have to prove before a state medical board that the procedure was medically necessary.
Opponents of the ban claim that the abortion procedures described are overwhelmingly used in emergencies, and that the prospect of having to defend a medical decision under threat of fine or imprisonment will hamper doctors' judgments.
In one form or another, the issue has been before Congress since 1995. Former President Clinton twice vetoed different forms of the measure.
The vast majority of abortions occur relatively early in pregnancy. According to the Centers for Disease Control and Prevention, roughly 58 percent of abortions take place before the end of the eighth week of gestation. Eighty-eight percent take place by the end of the 12th week.