The U2 singer was presented with the Free Your Mind Award and heard the United Nations Secretary General Kofi Annan praise his efforts to cancel Third World debt.
Mr Annan said in a pre-recorded broadcast: "Bono, as an artist, activist, and advocate for the poor, you have made a real difference, crossed boundaries and have broken taboos."
On being presented the award Bono by the Rolling Stones singer, Mick Jagger, the Irishman said: "This is going to make me worse."
The 17-year-old American pop singer Britney Spears won four MTV Europe Music Awards, one for each category she had been nominated in. She beat off competition from long-established stars such as Madonna to win Best Pop Act, Best Female Performer, Best Breakthrough Act and Best Song for Baby One More Time.
The awards host, Ronan Keating, twice found himself on the winners rostrum: Boyzone were declared Best UK and Ireland Act; By Request won the prize for Best Album.
British acts also shone. Fatboy Slim was awarded the Best Dance accolade and Blur won the Best Video category for "Coffee And TV".
Backstreet Boys won one of the four awards they were nominated for - Best Band - while American band The Offspring came out top in the Best Rock category.
The actor and rapper Will Smith won his first award since 1997, voted the Best Male Performer while Eminem won the Best Hip Hop act.
Whitney Houston, one of the performers in last night's pounds 3m ceremony at the Point Theatre, beat Lauryn Hill, Mariah Carey, Jennifer Lopez and TLC in the Best R & B section.
The two-hour show was the biggest televisual event staged in Ireland - with a potential audience of a billion people. Stars who performed on stage included The Cardigans, Mariah Carey, The Corrs, Jamiroquai, Puff Daddy, and Iggy Pop. The guest presenters included the actor Pierce Brosnan and the singer Geri Halliwell.