The 52-year-old singer became the first black woman to receive the honour.
Before presenting Jackson with the award, R&B singer Bruno Mars told the crowd she "represents undeniable artistic genius."
A retrospective documenting Jackson's career followed, with clips of her appearance as a kid on The Carol Burnett Show to highlights of her breakout hits.
Jackson then took the stage, performing "Nasty" from 1986's Control and "If" and "Throb" from Janet.
"I believe that for all the challenges, for all our challenges, we live at a glorious moment in history," Jackson said.
"It’s a moment when at long last women have made it clear that we will no longer be controlled, manipulated, or abused. I stand with those women and with those men equally outraged by discrimination who support us in heart or mind."
Jackson's honour comes just days after the 25th anniversary of her seminal album Janet, along with an appearance on the cover of Billboard Magazine.
Past recipients of the Icon Award include Cher, Celine Dion, Jennifer Lopez and Prince.
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