The pop superstar won Video of the Year for Formation, the most controversial work of her career, as she took home eight of the 11 awards for which she was nominated.
Formation, the first single off her intertwined film and album Lemonade, was shot in New Orleans and inspired by the city's Creole culture, its bounce hip-hop scene and the aftermath of Hurricane Katrina.
"I dedicate this award to the people of New Orleans. God bless you guys," Beyoncé told the gala at New York's Madison Square Garden.
Beyoncé stole the spotlight by performing for more than 16 minutes songs from Lemonade, managing even to change outfits in a set that culminated in the stage erupting in fire.
In one of the most striking moments, a series of gun-shots rang out as her dancers, in angelic white dresses, each dropped to the ground in a red fog.
The video for Formation, directed by Melina Matsoukas, had offered solidarity with the Black Lives Matter movement against police brutality with officers portrayed raising their hands as if under arrest.
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Beyoncé invited to the show, the mothers of four young African American men whose deaths have galvanized the United States -- Michael Brown, Eric Garner, Oscar Grant and Trayvon Martin.
Martin, 17, was killed in 2012 by a white neighborhood guard, a catalyst moment for Black Lives Matter. Brown, Garner and Grant were all killed by law enforcement.
Singer Alicia Keys offered another of the night's powerful moments as she recited a poem inspired by civil rights hero Martin Luther King Jr. who delivered his landmark I Have a Dream speech in Washington 53 years ago Sunday.
In a year marred by global conflict and a bitter US presidential race, Keys, moving seamlessly from spoken word to a cappella, said: "If war is holy and sex is obscene, then we got it twisted in this lucid dream."
"Maybe we can love somebody / instead of polishing the bombs of holy war."
At eight awards, Beyoncé tied her contemporary Lady Gaga and Norway's a-ha -- a sensation in MTV's early years -- for the second biggest win in a single night.
Peter Gabriel retains the record, set in 1987 after his animation-driven Sledgehammer.
In one of the night's most anticipated moments, rap superstar Kanye West -- who last year used the occasion to declare his intention to run for president in 2020 -- delivered a nearly stream-of-consciousness speech about empowerment.
As the audience chanted his stage-name Yeezy, West likened his creative talent to that of Apple founder Steve Jobs and entertainment pioneer Walt Disney, and said that unnamed wealthy white people had warned him not to make the comparison.
He defended his Famous, also up for Video of the Year, which depicted clean-cut pop star Taylor Swift naked in bed with him despite her complaints about the song.
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Also seen naked with West in the video are Republican presidential contender Donald Trump, known for his hardline anti-immigration stance, and fashion editor Anna Wintour.
"We came over in the same boat. Now we all in the same bed," West said, before clarifying that the on-screen lovers arrived on "maybe different boats."
West then presented a racy new video for his song Fade featuring actress and singer Teyana Taylor, who moved her body sensually in a gym before a steamy shower scene.
The video marked a theme in the evening, if accidental, of sexualized exercise.
Ariana Grande and Nicki Minaj received roars of crowd approval for a sensual take on a workout, with the pop singer and rapper dancing together in a stage transformed into a gym full of highly physical young men.
Drake won in the rap category for Hotline Bling, one of the most popular songs of the year.
But Drake did not appear to accept the award. According to the presenter, rap icon Puff Daddy, the Toronto star got stuck in New York traffic.
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Drake however did show up to present the Video Vanguard Award -- named after late King of Pop Michael Jackson -- to Rihanna, in recognition to her contributions to pop culture.
Drake gushed that Rihanna was "someone I've been in love with since I was 22."
The 28-year-old Rihanna put on four medleys of her songs throughout the show in outfits that began with a snug white T-shirt.
In an acceptance speech, Rihanna pledged never to forget her native Barbados.
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