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The 30-year-old actor scooped the Best Actor in a Motion Picture (Musical or Comedy) award for his performance in Elton John biopic Rocketman.
Speaking on stage, Taron said: "I'm so honoured to be nominated alongside legitimate icons and also Roman [Griffin Davis], who is an incredible kid.
"To Elton John - thank you for the music, for living a life less ordinary and for being my friend."
The Birkenhead-born actor fought off stiff competition from Hollywood royalty, including Leonardo DiCaprio and Daniel Craig, no doubt making his victory all the sweeter.
Rocketman also won the award for Best Original song with '(I'm Gonna) Love Me Again'.
The film was also nominated for Best Motion Picture, but lost out to Once Upon A Time In Hollywood.
Taron has become friends with Sir Elton, having been pictured with him at various events, including the BAFTA tea party on Saturday.
He shared a photo on Instagram of himself with the singer, with the caption: "Reunited at the @bafta tea party yesterday. Big day today. Win or lose it's all about the ride. And this has been the best. Love to all involved. So proud."
Other big winners at the awards include Joaquin Phoenix, who won best actor in the drama category for his dark portrayal of the Joker. The actor beat the likes of Christian Bale and Adam Driver for the coveted prize.
He played the troubled character in what was one of the year's most-anticipated - and highest grossing - movies.
It was also a big night for Quentin Tarantino, whose latest release Once Upon A Time In Hollywood was nominated for five awards.
Tom Hanks deservedly won the Cecil B. DeMille Lifetime Achievement Award, and he got a bit emotional in the process.
He told the audience: "I have a cold the size of Merv Griffin's Jeopardy! royalties."
Hanks also paid tribute to his family: "A man is blessed with a family sitting down front like that - a wife who is fantastic in every way, who has taught me what love is... five kids who are braver and stronger and wiser than their old man."