MTV said West, who was spotted earlier on the red carpet drinking alcohol, was ejected from an awards show already known for its circus-like atmosphere. West received loud boos from the crowd when his name was mentioned later in the show.
West apologized on his website. "I'm sooooo sorry to Taylor Swift and her fans and her mom," he wrote. "... I'm in the wrong for going on stage and taking away from her moment!"
Beyonce took the show's top honor -- video of the year -- for her single "Single Ladies (Put a Ring on It)" before recalling her first MTV award with her old band, Destiny's Child, and calling back Swift to the Radio City Music Hall stage to finish her acceptance speech.
"I would like Taylor to come out and have her moment," she said, before the country music star reappeared and thanked her fans.
MTV said Beyonce, Lada Gaga and Green Day won three awards apiece, the most of any artists on this year's awards show.
The cable channel's awards show began with a tribute to Jackson less than three months after the man known as the King of Pop died from what authorities call a prescription drug overdose at age 50.
"Most of us had turned our backs on him," Madonna said in a speech at the beginning of the awards that recalled his lost childhood. "He was so unique, so original, so rare and there will never be anyone like him again. He was the king."
Performers dressed like Jackson filled the stage and danced to some of his hit songs including "Thriller," "Bad" and "Smooth Criminal."
Janet Jackson then appeared on stage. With the video for her brother's song "Scream" playing on a screen behind her, she mimicked his dance moves in unison with the video. She did not speak.
Michael Jackson promoted many of his ground-breaking videos on MTV in the 1980s.
The network also aired a trailer for "This Is It," a documentary about Jackson due out in October that features footage from Jackson rehearsing for his comeback concerts.
The show's other top awards went to U.S. dance music star Lady GaGa, who won best new artist for "Poker Face." Rapper T.I. featuring Rihanna won best male video for "Live Your Life," and Britney Spears cemented her successful comeback winning best pop video for "Womanizer."
Eminem won best hip-hop video for "We Made You," and Green Day took the best rock video award for "21 Guns."
The show's performances included Pink, who wowed the audience singing while twirling on a trapeze high above the crowd. Lady Gaga performed her song "Paparazzi" while smeared with fake blood.
Some of the biggest cheers came after Beyonce performed her award-winning single surrounded by dozens of female dancers.
The night ended with a final reference to Swift, with the show's host, British comedian Russell Brand, joking he would give her "a shoulder to cry on."
(Additional reporting by Dean Goodman and Lucas Jackson; editing by Will Dunham)
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