The actor won for his role of Arthur Fleck, a variation of the same DC villain that Ledger played in Christopher Nolan’s film The Dark Knight.
Ledger went on to win a posthumous Best Supporting Actor Oscar for the performance.
Phoenix, who is favourite to win Best Actor at the 2020 Oscars, which take place in February, said: “I am standing here on the shoulders of my favourite actor Heath Ledger.”
Daniel Day-Lewis previously paid tribute Ledger at the same awards ceremony shortly after the actor’s death in 2008.
Many are praising Phoenix for the touching moment on Twitter.
Meanwhile Brad Pitt won Best Supporting Actor for his role in Quentin Tarantino’s Once Upon a Time in Hollywood and had the crowd – including his ex-wife Jennifer Aniston – in laughter over a joke about his failed marriages.
Bong Joon-ho’s South Korean film Parasite made history by becoming the first foreign language film to win the evening’s top prize.
The Oscars take place on 9 February.