According to People, the actor, who dated Portman in 2006, jokingly pointed out his ex-girlfriend's flaws before presenting her with the Desert Palm Achievement Award.
"She's a vegan, which makes it really frustrating when you're picking a place to eat," Gyllenhaal said.
He continued: "She's also recently announced that she's going to be a mum, and her child will probably need therapy after seeing Black Swan."
Gyllenhaal also praised Portman, saying: "Natalie is the Audrey Hepburn of our generation."
Portman is expected to earn an Oscar nomination for her role as a competitive ballerina in Black Swan.