Phoenix picked up a gong in the prestigious category Best Performance by an Actor in a Motion Picture - Drama for his starring role in Joker to rapturous applause from most of those around him.
But Beyonce was spotted staying firmly in her seat as the winner made his triumphant walk up to the stage, with stars including Leonardo DiCaprio and Reese Witherspoon all standing up in celebration of him.
Some of those watching the ceremony took to Twitter to air their disappointment at the singer, although others speculated that the sheer size of her voluminous dress had stopped her from getting to her feet.
She was also criticised for turning up an hour late to the awards ceremony and then spending time posing on the red carpet with husband Jay Z.
Phoenix’s portrayal of the Joker involved playing him as a comedian with mental health issues whose life spiralled out of control after being treated poorly by society.
He was up against Christian Bale, Antonio Banderas, Adam Driver and Jonathan Pryce for his award, although Joker lost out to 1917 in both the Best Motion Picture and Best Director categories.
The actor’s acceptance speech kept the censors busy as they had to bleep out his swearing, but he emotionally thanked his fiancee Rooney Mara for her support.
Winning in the Best Performance by an Actress in a Motion Picture - Drama category was Renee Zellweger for Judy, while the Supporting Role prizes were won by Laura Dern for Marriage Story and Brad Pitt for Once Upon a Time in Hollywood.