He was up against the likes of Bradley Cooper, Willem Dafoe, Lucas Hedges and John David Washington to get the award, and it's a testament to his talent that he came out on top.
After the initial shock of the win settled in, the 37-year-old actor did what everyone does at a ceremony like this does and thanked a whole bunch of people involved in the project. However, he made a particular effort to thank the one person who made this whole thing possible - the man himself, Freddie Mercury.
Malek closed out his speech by thoughtfully dedicating his award to the man he played on screen.
He said: "Thank you to Freddie Mercury for giving me the joy of a lifetime. I love you, you beautiful man. This is for and because of you, gorgeous."
Rami also paid tribute to the surviving members of Queen, guitarist Brian May and drummer Roger Taylor, who still tour with singer Adam Lambert taking vocal duties. Rami sat with May and Taylor for the duration of the glitzy ceremony. He thanked them 'for ensuring that authenticity and inclusivity exists in music and in the world and all of us'.
Following his impressive win, all eyes were set on the Best Picture Award, which coincidentally also went to Bohemian Rhapsody. A pretty good night for those involved with the movie and its production!
Executive producers Graham King and Jim Beach accepted the award, telling the crowd, much in the same way Malek did, what Mercury and the iconic band he fronted meant to them.
"The power of movies is that it brings us all together," he said.
"Freddie Mercury and Queen did that so successfully through their music and that's what we always wanted to accomplish in the cinemas. To see that magic come alive and to see the incredible response of this film has been truly humbling to everyone."
They praised their star Rami Malek for his portrayal of Freddie and his dedication to the role, which involved Rami staying in character a lot even off-camera. They concluded their speech by saying: "And finally to Freddie Mercury, thank you for showing us the power of embracing your true self. This one is for you. Thank you so much."
Malek has been widely praised for his portrayal of Mercury, by Queen fans, the general public, and movie critics. Perhaps the highest praise of all came from a little closer to home - Freddie's former guitarist and creative partner, Brian May.
Brian May recently told the Press Association: "He inhabited Freddie to the point where we even started to think of him as Freddie. Really remarkable."
It must be pretty overwhelming to receive that praise from someone who knew the icon so well.
Congratulations on your success, Rami. I'm sure Freddie would be proud.