WASHINGTON — Michèle A. Flournoy, an experienced military policymaker and mentor to scores of women in national security, may now be remembered as the first female secretary of defense who wasn’t. Three times.

For months Ms. Flournoy — who repeatedly sat at the center of heated disputes as the under secretary for policy at the Pentagon during the Obama administration — was widely believed around Washington to be a front-runner for President-elect Joseph R. Biden Jr.’s pick for the top job.

On Monday, however, aides to Mr. Biden revealed that he instead would nominate retired Gen. Lloyd J. Austin III, a former commander of the American military effort in Iraq, to lead the Pentagon, deflating a narrative of inevitability that many around her sought to build even before Mr. Biden won. If confirmed, General Austin would be the first Black defense secretary in the nation’s history.

The decision enraged many of the women Ms. Flournoy elevated from the trenches of the male-dominated world of national security, who were hoping to see another woman in a prominent cabinet post. (Mr. Biden has selected the first female vice president and roughly equal numbers of men and women for cabinet-level jobs so far, but many of the most senior roles, including secretaries of state, defense and homeland security, have gone to men.)

The job of defense secretary will need both public relations and practical retooling after four turbulent years under President Trump, and as the number of women in the military continues to grow, many had hoped Ms. Flournoy, who was considered for the role twice before, would be the one to do it.

“Flournoy is just beloved,” said Rosa Brooks, a law professor at Georgetown University Law Center who was one of Ms. Flournoy’s subordinates at the Pentagon and played a role in the aggressive public lobbying in her favor.

“The first Black secretary of defense is also something to celebrate,” she added, “but Flournoy occupies a special place in the pantheon of defense experts.”

On Tuesday, Ms. Flournoy congratulated General Austin, calling him “a colleague and friend.”

“I know he will bring his impressive skills to bear to lead all those who volunteer to defend our country, military and civilian, at this critical moment in our nation’s history,” she said in a statement. “I look forward to helping him and the president-elect succeed in any way that I can.”

Several people involved in or close to Mr. Biden’s transition team now say that the notion of Ms. Flournoy as the front-runner was mostly a product of an impressive lobbying campaign by her supporters — many but by no means all women — in public statements, published opinion pieces and tweets in recent weeks.

Ms. Flournoy’s résumé had seemed potentially right for the moment. She served in the Pentagon first under President Bill Clinton, and from 2009 to 2012 she was the under secretary of defense for policy in the Obama administration — the highest-ranking role for a woman in the Pentagon at the time. She removed her name from contention for the top job in 2014, when Mr. Obama initially was considering her to succeed Defense Secretary Chuck Hagel.

She instead became a senior adviser at the Boston Consulting Group, then went on to help found WestExec Advisors, a consulting firm. Her second shot at the job was scuttled when Hillary Clinton — who was widely expected to name her — lost the presidential election in 2016.

Ms. Flournoy was known for seamlessly moving between the civilian and active-duty sides of the Pentagon, bridging the often impenetrable gap between those in uniform and those in suits — a skill that some fear may be lost with a retired general in the role. She did so, her fans said, by translating the political imperatives of civilians to the active-duty military world and carefully helping the civilian side understand the military’s practical needs and limitations in seeing through the policy goals of elected officials.

“She is enormously talented, and the last thing I think about is that she is a woman,” said Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff at the time of the Afghanistan surge, which she helped advocate to the Obama White House. “From my perspective that is a great thing.”

Yet among women who toil in the national security trenches, an area where men — and what Ms. Flournoy often refers to as their “mini-mes” who succeed them — have historically dominated, Ms. Flournoy is widely regarded as an essential mentor.

“An entire generation of national security women used her as their role model in how to navigate a male-dominated job,” said Representative Elissa Slotkin, Democrat of Michigan, who also worked for Ms. Flournoy. “The lesson she provided for women is that you have to always be the best prepared in the room. I literally learned that from her, and I now pass that down to the young women who work for me.”

Celeste Wallander, the president of the U.S.-Russia Foundation, is among scores of women who consider Ms. Flournoy central to their successful careers. Ms. Wallander recalled a time in 1989 when the two were both academics at Harvard, where Ms. Wallander, very junior, was usually left off the invitation list for dinners and other events with major players in her field. Ms. Flournoy quietly had her added to the lists. “I got to meet people because I was at the table now,” Ms. Wallander said.

Ms. Flournoy was also popular for her decision, after studying business literature on the workplace, to give exhausted Pentagon personnel “planned time off,” with each covering for one another as they took scheduled breaks to care for children, visit parents, train for a marathon, schedule appointments or whatever they wished.

But even her supporters acknowledge that Ms. Flournoy’s WestExec consulting role, and her position as an adviser to the investment fund Pine Island Capital Partners, put her in the cross hairs of many liberal critics, something her business partner in those roles, Antony J. Blinken, seemed to escape when Mr. Biden announced him as the nominee for secretary of state.

Another possible source of tension was that Mr. Biden differed greatly with many in the Obama White House over the surge in Afghanistan.

In 2009, Ms. Flournoy, in her role as under secretary for policy to Robert M. Gates, the Pentagon chief at the time, met with Gen. Stanley A. McChrystal at an airfield near Mons, Belgium, to hear the general make his case for a large troop increase in the region — something Mr. Biden, then the vice president, deeply and openly opposed.

The political conflict over that war, and statements criticizing Mr. Biden attributed to General McChrystal’s aides, would later cost General McChrystal his job as commander in Afghanistan.

Mr. Biden is said to have sought a defense secretary with whom he has a personal and natural alliance.