The awards extravaganza at Radio City Music Hall in New York saw Beyonce´s "Single ladies" win the MTV award, known as a Moonman, for best video of the year.
There were Moonmen for Britney Spears in pop video, Green Day in rock and Eminem for hip hop, while drama queen Lady Gaga, who changed costume several times during the show, was picked as best new artist.
Teen country star Taylor Swift won best female video, but her acceptance speech was spoiled when rapper Kanye West crashed the stage and grabbed her microphone to tell the hall he favored Beyonce´s video.
Beyonce later made up for the thuggish incident by inviting Swift to share the stage during her own award triumph.
However, it was Jackson, who died aged 50 on June 25, receiving most accolades, with host Russell Brand and award winners lining up to pay tribute.
Madonna kicked off the evening by commemorating "one of the greatest talents the world has ever known."
Jackson "didn´t just make you want to dance," the diva said in her moving and personal remarks, "but actually made you believe you could fly."
But after praising Jackson, Madonna sounded a darker note, saying she felt many failed to go to his help when his life began to fall apart amid health problems, a fading career, and child abuse allegations.
"I had abandoned him," she said. "We had abandoned him, that we allowed this magnificent creature who lit the world on fire to somehow slip through the cracks."
"Most of us had turned our backs on him," she said, before ending with the call: "Long live the king!"
Janet Jackson then recreated the dance moves from her only video made with her brother, "Scream," as a vast screen behind her played the original.
Brand, a British comedian who appeared in a top hat, also spoke for the late pop giant, saying: "Tonight is dedicated to the great Michael Jackson."
Los Angeles coroners say Jackson´s death is being treated as a homicide, but prosecutors have not filed charges so far.
2009 MTV video awards winners
Video Of The Year: Beyonce "Single Ladies (Put A Ring On It)"
Best New Artist: Lady Gaga "Poker Face"
Best Hip-Hop Video: Eminem "We Made You"
Best Male Video: T.I. f/ Rihanna "Live Your Life"
Best Pop Video: Britney Spears "Womanizer"
Best Rock Video: Green Day "21 Guns"
Best Female Video: Taylor Swift "You Belong With Me"
Related story
Michael Jackson’s estate and former manager settle lawsuit
