Kunis beat out Michael Fassbender (12 Years a Slave), Barkhad Abdi (Captain Phillips), Benedict Cumberbatch (Star Trek Into Darkness), and Donald Sutherland (Catching Fire) for the top prize.
"This is, by far, the coolest award," she told the audience. "And I just realized I was the only woman nominated, and I won! So thank you guys."
The 30-year-old actress is reportedly expecting her first child with fiancé Ashton Kutcher.