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The 45-year-old actor took to the stage to pick up the accolade for Outstanding Performance by a Male Actor in a Leading Role at the SAG Awards.
Paying tribute to Ledger - who portrayed the Joker in The Dark Knight before he passed away on 22 January 2008 - Joaquin told the audience: "Really I'm standing here on the shoulders of my favourite actor, Heath Ledger. So thank you and goodnight."
Responding to Phoenix's tribute, one fan took to Twitter saying: "Let me just please cry in peace. Heath would have been so proud of what you did, Joaquin."
Another added: "Wow I love that he paid homage to Heath Ledger. Congratulations, Joaquin."
Earlier in his speech, the five-time nominee said: "I was here many years ago and I couldn't fully appreciate it at the time. I now realise how fortunate I am to be a part of this community, I have such reverence for actors and what we do.
"I'd like to just talk a little bit about my fellow nominees if that's OK. When I started acting again and going to auditions, I'd always get to like the final call back and I think many people know what that's like.
"There would always like two other guys that I was up against and we would always lose to this one kid. No actor would ever say his name because it was too much, but every casting director would whisper 'it's Leonardo' [DiCaprio].
"Who is this Leonardo? Leonardo, you have been an inspiration for over 25 years to me and so many people - I thank you very, very, very much."
He went on: "Christian [Bale], you commit to your roles in ways that I could only dream of. You never turn in a bad performance, it's infuriating. I wish you would one time - just suck once, it'd be great.
"Adam [Driver] I've been watching you the last few years and you've been turning in these beautiful, nuanced, incredible, profound performances and I'm just so moved by you and you were just devastating in this film [Marriage Story]."
Addressing Taron Egerton for his role in Rocketman, he said: "You're so beautiful in this movie and I'm so happy for you and I can't wait to see what else you do."
What a LAD.
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