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. Her bill 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 were 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.
Thursday's rejection is unlikely to be the final word. Defeated but unyielding, Gillibrand and her allies vowed to seize the next opportunity to force another vote, probably in the spring when the Senate starts 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.
"We will not be stopped. Look, I've been here long enough to see how sometimes change is painful and slow. But it happens. I've seen it. And we will see it again," said Sen. Barbara Boxer, D-Calif.
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 people, mostly women, may have been sexually assaulted in the most recent accounting with thousands unwilling to come forward for fear of inaction or retribution.
"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 were Republican leader Mitch McConnell, who faces Democratic challenger Alison Lundergan Grimes in his re-election bid, and Mike Enzi of Wyoming.
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.
In two hours of debate, proponents and opponents argued on the Senate floor based on personal experiences, growing frustration with what they dismissed as fixes around the edges and horrific stories from the ranks.
"The current system is failing the men and women in uniform," said one of the Senate's newest members, John Walsh, D-Mont., who spent 33 years in the Montana National Guard and is the first Iraq War veteran in the body. "We have moved too slowly."
On the other side was Sen. Jack Reed, D-R.I., a West Point graduate who served in the 82nd Airborne Division as an infantry platoon leader and company commander. Reed said stripping commanders of the authority to discipline the troops would be "detrimental to the effectiveness of the force and common goal to reduce sexual assault."
After blocking Gillibrand's bill, the Senate moved toward overwhelmingly passage of a measure sponsored by McCaskill and two Republican senators—Kelly Ayotte of New Hampshire and Deb Fischer of Nebraska. That bill would eliminate the "good solider defense"—that a service member's character and military performance can be used in a case—unless it is directly connected to the allegation. And it would allow sexual assault victims to challenge their discharges or separation from service.
The bill also calls for a civilian service secretary review if a prosecutor and commander disagree over whether to litigate a case.
The Senate voted 100-0 to move ahead on that bill. A vote on passage is scheduled for Monday.
Three months ago, Congress cleared and President Barack Obama signed a defense policy bill that included several changes to military law, including stripping commanders of their ability to overturn jury convictions and criminalizing retaliation against victims who come forward about sexual assaults.
The Pentagon came under pressure last month to disclose more information about how sexual assault cases are adjudicated following an Associated Press investigation that found a pattern of inconsistent judgments and light penalties for sexual assaults at U.S. bases in Japan.
Gillibrand, who chairs the Senate Armed Services personnel subcommittee, called on Defense Secretary Chuck Hagel in a Feb. 10 letter to turn over case information from four major U.S. bases: Fort Hood in Texas, Naval Station Norfolk in Virginia, Camp Pendleton Marine Corps base in California and Wright-Patterson Air Force Base in Ohio. Such records would shed more light on how military commanders make decisions about courts-martial and punishments in sexual assault cases and whether the inconsistent judgments seen in Japan are more widespread.
The AP's investigation, which was based on hundreds of internal military documents, found that what appeared to be strong cases were often reduced to lesser charges. Suspects were unlikely to serve time even when military authorities agreed a crime had been committed. In two rape cases, commanders overruled recommendations to court-martial the accused and dropped the charges instead.
The Army is investigating sexual abuse allegations against an officer who trains military prosecutors who handle sexual and physical abuse cases. Lt. Col. Joseph Morse is accused of groping a female Army lawyer while both were attending a legal conference in Northern Virginia in 2011, according to a senior defense official.
Associated Press writers Richard Lardner and Andrew Taylor contributed to this report.