WASHINGTON — Bowing to the Pentagon, the Senate agreed after impassioned debate Thursday to leave the authority to prosecute rapes and other serious crimes with military commanders in a struggle that highlighted the growing role of women in Congress.

The vote was 55-45 in favor of stripping commanders of that authority, but that was short of the 60 necessary to move ahead on the legislation sponsored by Sen. Kirsten Gillibrand. It would have given the decision to take serious crimes to courts-martial to seasoned military trial lawyers, independent of the chain of command.

The debate and vote was the culmination of a nearly yearlong campaign to curb sexual assault in the ranks, led by female senators who have questioned whether the military’s mostly male leadership understands differences between relatively minor sexual offenses and serious crimes that deserve swift and decisive justice.

Pentagon leaders vigorously opposed the measure, as did former prosecutors and military veterans in the Senate who argued that commanders should have more responsibility, not less, for the conduct of the men and women they lead in war and peacetime.

“We can’t let the commanders walk away,” insisted Sen. Claire McCaskill of Missouri, who bemoaned the tenor of a policy debate that pitted her against fellow Democrat Gillibrand.

Backers of the measure insisted that piecemeal reforms have had only a limited impact on a problem that even the military has called an epidemic. Survey results have suggested that some 26,000 women may have been sexually assaulted in the most recent accounting with thousands unwilling to come forward for fear of inaction or retribution.

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“The people who don’t trust the chain of the command are the victims,” Gillibrand said.

The New York lawmaker was relentless in lobbying her colleagues, even in the final minutes of the vote. Standing in the well of the Senate, she tried to persuade a wavering Sen. Mark Kirk, an original sponsor of her measure. Kirk also got an earful from Sen. John McCain, R-Ariz., arguing against the measure.

Kirk, an Illinois Republican, said after the vote that he was concerned the bill would “jeopardize our readiness and our military stationed in the field.”

Among the Republicans voting with Gillibrand was Mitch McConnell, who faces Democratic challenger Alison Lundergan Grimes in his re-election bid.In fact, Gillibrand’s effort divided the Senate in ways that smashed conventional lines on both gender and political party.

Conservative Sens. Ted Cruz of Texas and Rand Paul of Kentucky backed her effort, while the chairman of the Armed Services Committee, Democratic Sen. Carl Levin of Michigan, opposed it. Including Gillibrand, the bill had the support of 17 of the Senate’s 20 women.

The rejection was unlikely to be the final word on the issue. Gillibrand is expected to pursue it this spring when the Armed Services Committee begins work on a sweeping defense policy bill for the 2015 fiscal year.

“Many people said to me, ‘Kirsten, I’m going to watch this, and if it doesn’t get better in the next six months, I’m with you next time,’ ” she said at a news conference.

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