Last year's Best Actor winner J.K. Simmons presented The Danish Girl star with the 2016 Oscar for Best Supporting Actress at this year's ceremony.
When the first-time Oscar nominee's name was announced, a shocked Vikander turned to her Oscar-nominated beau, Michael Fassbender, and gave him an adorable kiss before heading to the stage.
Vikander thanked nominated costar Eddie Redmayne during her acceptance speech.
"Eddie, thank you for being the best acting partner I could have!" Vikander, 27, said through tears. "I never could have done it without you. You raised my game."
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Vikander took the trophy from a field that included The Hateful Eight's Jennifer Jason Leigh, Carol's Rooney Mara, Rachel McAdams from Spotlight and Kate Winslet in Steve Jobs.
The 88th annual Academy Awards, hosted by Chris Rock, are being presented live on ABC from the Dolby Theatre in Hollywood, California.