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The 45-year-old joins fellow nominees Adam Driver (Marriage Story), Leonardo DiCaprio (Once Upon a Time... in Hollywood), Jonathan Pryce (The Two Popes), and Antonio Banderas (Pain and Glory) in the running for recognition from the Academy heading into the 92nd edition of the annual awards.
The ceremony will take place at Los Angeles' Dolby Theatre on 9 February.
He's already picked up the Golden Globe award for Best Actor, and last night also collected the Critics' Choice Award as well.
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."
If he is successful, this will be Phoenix's first Academy Award, despite past nominations for his performances in Gladiator, Walk The Line and The Master.
This Oscar nomination is his first in seven years.
Joker director Todd Phillips and composer Hildur Guðnadóttir have also received nominations, while the film is also in the running for Best Picture.
The movie was also a smash 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.
The film itself is a dark, standalone look into the origins of Batman's nemesis, and uncovers the story of a man rejected by society. It explores what made him into the seemingly heartless man familiar to fans of the Batman movies, TV shows and comic books.
We follow failed comedian and clown Arthur Fleck as he descends into psychopathy after society turns against him. After taking one too many knocks, Fleck becomes The Joker, the Clown Prince of Crime, and begins his campaign of terror against Gotham City.
Well, it looks like Joaquin Phoenix is going to get the recognition that Fleck never did.
Here are the big hitters from the 2020 Academy Award nominations:
Best Picture - Ford v Ferrari/Le Mans '66, The Irishman, Jojo Rabbit, Joker, Little Women, Marriage Story, 1917, Once Upon a Time... in Hollywood, Parasite
Best Director - Martin Scorsese for The Irishman, Todd Phillips for Joker, Sam Mendes for 1917, Quentin Tarantino for Once Upon a Time... in Hollywood, Bong Joon-ho for Parasite.
Best Actress in a Leading Role - Cynthia Erivo for Harriet, Scarlett Johansson for Marriage Story, Saoirse Ronan for Little Women, Charlize Theron for Bombshell, Renée Zellweger for Judy.
Actor in a Supporting Role - Tom Hanks for A Beautiful Day in the Neighborhood, Anthony Hopkins for The Two Popes, Al Pacino for The Irishman, Joe Pesci for The Irishman, Brad Pitt for Once Upon a Time... in Hollywood.
Actress in a Supporting Role - Kathy Bates for Richard Jewell, Laura Dern for Marriage Story, Scarlett Johannson for Jojo Rabbit, Florence Pugh for Little Women, Margot Robbie for Bombshell.
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