Brown beat out Kid Rock and Usher for the male artist honor.
"I just want to thank first and foremost all the fans that supported me from Day 1," Brown said upon accepting his award.
The prize was presented by socialite-actress Paris Hilton and hip-hop artist T-Pain, who put his arm around Hilton and told the crowd she wasn't single any more and that they were witnessing a "new beginning."
"In your face corporate America," he declared.
Hilton recently broke up with her musician boyfriend Benji Madden.
Brown later won the night's top honor of artist of the year. Also nominated in that category were Alicia Keys, Coldplay, Eagles and Lil Wayne.
Keys won the pop/rock album award for "As I Am." Her CD was selected over offerings from Eagles and Coldplay.
However, Keys lost the prize for favorite female pop/rock artist to Rihanna. Mariah Carey was also up for the trophy.
Rihanna won the award for favorite female soul/R&B artist, as well, while Daughtry picked up the trophy for favorite pop/rock band, duo or group.
The 36th annual AMA show featured performances by New Kids on the Block, Pink, Taylor Swift, Leona Lewis, Miley Cyrus and Coldplay.
Keys and Queen Latifah closed the show with a rendition of "Superwoman," which included a shout-out to their "The Secret Life of Bees" co-star Jennifer Hudson whose mother, brother and nephew were shot and killed last month.