The acting categories had shut out people of colour while no women directors were recognised in the directing segment.
"I don't think anybody wants a handout or preferential treatment, although that's what we give ourselves every year. I think people just want to be acknowledged, appreciated and respected for their work. This is not a self-righteous condemnation because I'm ashamed to say that I'm part of the problem," Phoenix said on stage at the Royal Albert Hall.
"I have not done everything in my power to ensure that the sets I work on are inclusive, but I think it's more than just having sets that are multicultural. We have to do the hard work to truly understand systemic racism. I think it is the obligation of the people that have created and perpetuate and benefit from a system of oppression to be the ones that dismantle it. So that's on us," he concluded.
Prince William, who presented this year's Bafta Fellowship to "Star Wars" producer Kathleen Kennedy, also addressed the issue.
"We find ourselves talking again about the need to do more to address diversity in the sector. That cannot be right in this day and age," he said.
"1917" also took home the Baftas for cinematography, production design, sound and special visual effects.
Actor Rebel Wilson took a potshot at the Academy for not nominating women directors. She said, "I don't think I could do what they do, honestly. I just don't have the b***s," as the room erupted in laughter.
Besides Phoenix's predicted win, Todd Phillips' "Joker" managed two more awards in the best original score and casting categories.
Actor Renee Zellweger took home the best actress honour for her role as legendary singer-actor Judy Garland in "Judy" and had a brief reunion with her "Bridget Jones" co-star Hugh Grant near the stage.
Grant, who was one of the presenters, joked, "First of all, well done Jones.That was a very silly little dress, I thought," the actor, who played the role of Daniel Cleaver in the movie, said.
Brad Pitt and Laura Dern continued their winning streak in the supporting categories as they bagged one more for their performances in Quentin Tarantino's revisionist period piece "Once Upon a Time in Hollywood" and divorce drama "Marriage Story", respectively.
In a reference to the UK leaving the European Union, Pitt said -- in a written note read by his "Once Upon a Time..." co-star Margot Robbie -- "Hey Brits, heard you just got single. Welcome to the club!"
"He's gonna name this Harry, because he's really excited about bringing this back to the States with him," Robbie said in another dig at the locals in light of Prince Harry and his wife Meghan Markle stepping down as senior royals as Prince William and wife Kate Middleton chuckled in the audience.
South Korean director Bong Joon-ho's "Parasite" scooped two Baftas -- for original screenplay and film not in the English language.
The award for best adapted screenplay went to writer-director Taika Waititi for "Jojo Rabbit".
"This is very, very cool for me. (I) come from the colonies. We know it's been a hard week for you guys," the New Zealander filmmaker began his acceptance speech.
Lifting the trophy, Waititi said, "It's been very nice to take a little bit of your gold, back home, where it belongs."
Jay Roach-directed "Bombshell", based on the accounts of several women at Fox News
who set out to expose CEO Roger Ailes for sexual harassment, picked up best hair and make-up trophies.
Greta Gerwig's adaptation of "Little Women" secured a win in the best costume category and "Ford v Ferrari", which released in the UK as "Le Mans '66", was adjudged the film with best editing.
Actor-director Andy Serkis was honoured with the outstanding British contribution to film award, which was presented to him by veteran theatre and film actor Ian McKellen.
Micheal Ward, known for "Top Boy" and "Blue Story", was named the Bafta rising star.
"Klaus" took home the best animation award and "Grandad was a Romantic" was named the best British short animation. "Learning to Skateboard in a war zone (If you're a girl)" won the best British short film award.
"Sama", a film about a young mother's experience of the Syrian civil war, won best documentary Bafta.
"Bait" was named outstanding debut by a British writer, director or producer.
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