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The 45-year-old picked up the gong at the 73rd British Academy Film Awards held at the Royal Albert Hall, London, tonight.
Collecting his award, Phoenix took a moment to discuss 'systemic racism' and the lack of diversity in Hollywood and this year's awards season.
"I feel conflicted because so many of my fellow actors that are deserving don't have that same privilege," he said.
"I think we send a very clear message to people of color that you're not welcome here.
"I don't think anybody wants a handout or preferential treatment, people just want to be acknowledged, appreciated and respected for their work. This is not a self-righteous condemnation. I'm part of the problem."
He continued: "We have to really do the hard work to truly understand systemic racism.
"I think that it is the obligation of the people that have created and benefited from a system of oppression to dismantle it.
"So that's on us."
Hotly-tipped to claim the coveted trophy, Phoenix fought off competition from some of the most respected actors around: Jonathan Pryce; Adam Driver; Taron Egerton; and Leonado DiCaprio.
Directed and written by Todd Phillips (The Hangover), Joker is a dark, standalone that looks into the life of Batman's arch nemesis.
Phoenix plays the troubled Arthur Fleck, a struggling clown who is cast aside by society and spirals into the depths of madness, eventually becoming the infamous Clown Prince of Crime and commencing his campaign of terror against the people of Gotham.
The film was an absolute smash hit at the box office. During the film's run in theatres it managed to rake in more than $1bn (£770m) worldwide. That's even more impressive when you consider that it only cost $62.5m (£48m) to make.
Just last month, Phoenix won the 'Best Performance by an Actor in a Motion Picture' award at this year's Golden Globes.
Accepting the prestigious award, he praised fellow actors, saying: "It's infuriating. I wish you (Christian Bale) would. Just suck once. Adam (Driver), I've been watching you the last few years and you've been turning in these beautiful, nuanced, incredible, profound performances. I'm just so moved by you...you should be here.
"Taron (Egerton), I'm so happy for you...you're so beautiful in this movie (Rocketman) and I'm so happy for you, and I can't wait to see what else you do."
He added: "I'm standing here on the shoulders of my favorite actor, Heath Ledger."
As well as his BAFTA and Golden Globe, Phoenix also picked up a Critics' Choice Award last month.
Speaking on stage after last night's recognition, Phoenix said: "Scott Silver and Todd Phillips, you checked us.
"You took a comic book character and used it to talk about childhood trauma, gun violence, isolation and mental health, and instead of inciting violence, you invited the audience in to see what it feels like when you're one of the forgotten."
He also paid tribute to his mum, adding: "I need to thank my mum. Mum, you've always been my greatest inspiration, even when self-pity led me astray.
"You've never given up on me and I deeply appreciate your support."
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