She received prizes for best female, best song ("Halo") and best video ("Single Ladies (Put a Ring on It") on one of pop music's biggest nights outside the United States.
"I have to dedicate this award to all the other beautiful artists," Beyonce said after being named best female, the second of her three prizes. "Thank you MTV for this wonderful honor."
To coincide with MTV's awards show, Irish rockers U2 treated 10,000 fans to a free concert in front of Berlin's Brandenburg Gate, where the music channel's first Europe Music Awards were held in 1994.
Lead singer Bono performed hits such as "One," "Sunday Bloody Sunday" and "Beautiful Day" during a 30-minute set and greeted the crowd in German with the words: "Berlin, Du bist wunderbar."
Beyonce's husband, hip hop star Jay-Z, was also a winner on the night, topping the best urban act category.
Wearing a black leather jacket and sunglasses, he referred to the theme of the Berlin Wall, saying: "I look forward to the day when all those walls come down."
The wall, a symbol of the Cold War that split the city, was opened on November 9, 1989, leading to the reunification of East and West Germany 11 months later.
U.S. DOMINATION
Beyonce took to the stage after her husband's acceptance speech, appearing in a red heart and wearing a scarlet bodice and garters to perform the hit "Sweet Dreams."
Best male act went to Detroit rapper Eminem, who thanked his supporters in a video message.
The winners are chosen by MTV viewers online, and the music channel, part of Viacom, said more than 100 million votes were cast in 2008. As the list of winners this year underlined, the MTV Europe Music Awards tend to be dominated by big U.S. names.
One of the few exceptions was Germany's Tokio Hotel, beating the likes of Black Eyed Peas and Kings of Leon to take the best group award.
Green Day, who performed the opening song on the night, were named best rock act.
The biggest losers on the night were Nashville-based Kings of Leon, who led the field with five nominations but came away empty-handed.
New Yorker Lady Gaga, renowned as much for her extravagant outfits as for her electro-dance-pop, was the only other act to garner five nominations. She won the best new act category.
U.S. singer Katy Perry, hosting the awards for the second year in a row, had promised a show inspired by the "Cabaret" film with Liza Minnelli, set in 1930s Berlin, and did not disappoint.
She appeared on stage in a bowler hat, bow tie, bodice and thigh-high boots, and performed a routine on chairs with eight cabaret dancers as glitter rained down on the stage.
Colombian pop star Shakira showed up in a glittery mini dress, black knee-length boots and long, blond locks to perform her hit "Did It Again," while British chart-topper Leona Lewis wore a flowing black gown for her rendition of "Happy."
There was a video tribute to the late king of pop Michael Jackson during the show.
(Writing by Mike Collett-White; editing by Andrew Dobbie)
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