LOS ANGELES — No one who has paid any attention to the Academy Awards over the past 89 years has ever seen anything like “Moonlight’s” shocking, exhilarating, stomach-churning come-from-behind Oscar win on Sunday night — a victory that stunned the Dolby Theatre audience and viewers watching around the world.

In a rare year when everything went bizarrely haywire at the last minute, triggering memories of Steve Harvey’s 2015 Miss Universe flub, as well as flashbacks to the recent historic upset in the presidential election, one statistical trend held steady: Not since Hilary Swank won the Oscar for “Million Dollar Baby” in 2005 have the awards for lead actress and best picture gone to the same movie.

The stage had seemed set for Emma Stone to break the trend this year as the lead-actress front-runner starring in the best-picture front-runner, “La La Land.” While some had anticipated an upset win by Isabelle Huppert for “Elle,” Stone’s road to victory seemed clear.

But then “Moonlight,” despite having lost the reliably predictive producers and directors guild awards to “La La Land,” pulled through with the win.

There are several possible takeaways here, not least among them the fact that Barry Jenkins’ film strikes me as the most deserving best-picture Oscar winner since “The Hurt Locker” and possibly “The Lord of the Rings: The Return of the King.” But there’s also the fact that, for all the encouraging talk of increased gender parity in front of and behind the camera, the motion picture academy still faces a perception problem in terms of which films, and which genders, are deemed significant enough for its highest honor.

Movies about men, such as “The King’s Speech,” “The Social Network,” “Lincoln” and “The Revenant,” don’t have to work hard to be taken seriously; their dramatic significance and mainstream appeal are assumed from the get-go.

To be fair, there have recently been several female-centric films that fulfilled the same requirements and were duly recognized for it. Brie Larson won last year for “Room,” an intimate and emotional two-hander that was also nominated for best picture and director. Portman won for carrying the multi-Oscar-nominated “Black Swan,” while Sandra Bullock took the prize for one best picture nominee (“The Blind Side”) and was nominated for another (“Gravity”). But for the most part, these feel like the exceptions that prove the rule.

Not for nothing did Cate Blanchett, accepting her Oscar for “Blue Jasmine” three years ago, rebuke “the idea that female films with women at the center are niche experiences.” That idea still persists. Unlike their male-dominated counterparts, films such as “Blue Jasmine” and “Still Alice,” to name a few recent lead-actress Oscar winners, are still largely treated as specialty items. They seem to have been conceived as showcases for their leading ladies’ technical brilliance, rather than as great movies in their own right.

Stone’s work in “La La Land” is different. She and Gosling met with plenty of criticism for their less-than-Juilliard-worthy singing and dancing, but the worth of Stone’s performance isn’t reliant on musical prowess alone. Her strengths as a performer — her sharp comic instincts and emotional sincerity, that piercing sense that the camera is seeing straight through to her soul — dovetail with the film’s own melancholy virtues. She isn’t at odds with the material; she’s beautifully in sync with it.

That Stone won for “La La Land” and Gosling didn’t is entirely fitting; this is very much her movie, and its most affecting moments belong to her. And that highlights still another phenomenon at work here, one that is actually cause for optimism: 2016 was an exceptional, fiercely competitive year for female leads and a relatively middling one for male leads.

Had the academy somehow not nominated Stone, Huppert, Negga, Portman and Streep for lead actress, they could have still served up a terrific lineup with, say, Amy Adams (“Arrival”), Annette Bening (“20th Century Women”), Rebecca Hall (“Christine”), Jessica Chastain (“Miss Sloane”), Taraji P. Henson (“Hidden Figures”) and many others.

Adams’ omission, in particular, remains one of the season’s biggest head-scratchers, not least because she headlined a film that the academy saw fit to nominate in eight categories, including best picture.

Finally, there’s the much-discussed fact that Viola Davis, the supporting-actress winner for “Fences,” was submitted in that less competitive race, despite playing a leading role. Had Davis, a three-time nominee, been campaigned as a lead, her shattering turn would almost certainly have been a threat to win.

The welcome, overbearing and extremely necessary discussion around the Oscars and diversity will continue, and in the future I hope the academy will show its willingness to give best picture to a female-led film. But Sunday night’s history-making flub aside, there should be no regret on the members’ behalf for awarding their top prize to “Moonlight,” a film about a young, black gay man that doesn’t re-entrench conventional notions about masculinity so much as subvert them entirely.

Writing about both “La La Land” and “Moonlight” a week ago, I wrote, “In the spirit of a less hostile, less Trumpian awards season, I’d suggest that these two fine movies, far from being natural adversaries, are in fact worthy companion pieces.”

None of us realized exactly how true that would be, how inextricably these two movies’ fortunes would be, up until the thrilling, devastating, only-in-Hollywood finale.

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