"Bohemian Rhapsody", which was released in India by Fox Star Studios, is a biopic on Mercury and the band Queen, and explores the rise of the band with a focus on the Indian-origin lead singer's personal life, his sexuality and the way he dealt with his fame.
Malek expressed his gratitude to the rock band, thanking them for allowing him to be a "tiny part of your phenomenal history". He also used his acceptance speech to address struggles of immigrants and the changing times in Hollywood.
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"Oh my god," Malek said as he got on the stage to receive the honour.
"My mom is in here somewhere. I love you. I thank my family. My dad didn't get to see this, but I am sure he is looking down on me,a he said as the camera panned towards his visibly emotional family.
"This is a monumental moment. I am so appreciative to all of you, who have had a hand to get me here. People who took a chance on me.
"I may not have been the obvious choice, but I guess it worked out,a said Malek thanking Fox and "everyone who believed in me. It's something I will treasure for the rest of my life," the actor said.
Malek also thanked Queen, saying "thank you for making me a tiniest part of your phenomenal and extraordinary legacy".
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"I am forever in your debt. I would also like Ato thank my crew and cast. You are my equals and better. I could have not been here without you."
Malek, who has Egyptian-American roots, remembered Mercury on stage.
"We made a film about a gay man, an immigrant, who lived his life just unapologetically himself," Malek said during his acceptance speech.
"The fact that I'm celebrating him and this story with you tonight is proof that we're longing for stories like this."
"I am the son of immigrants from Egypt, a first-generation American.
"And part of my story is being written right now. And I could not be more grateful to each and every one of you, and everyone who believed in me for this moment. It's something I will treasure for the rest of my life," Malek added
He was pitted against Christian Bale ("Vice"), Bradley Cooper ("A Star Is Born"), Willem Dafoe ("At Eternity's Gate") and Viggo Mortensen ("Green Book").