The sci-fi love story won the two main awards of the night, with del Toro taking home best director for what he called “a mad pitch”.
Gary Oldman and Frances McDormand won the main acting nods, also in line with expectations and betting odds, for their roles in Darkest Hour and Three Billboards Outside Ebbing, Missouri.
It was Oldman’s first ever Oscar win, and the Briton thanked the US for welcoming him years ago.
“I owe this and so much more to so many. I have lived in America for the longest time and I am deeply grateful to her. My home, my family and my Oscar,” he said in the acceptance speech.
“The movies, such is their power, captivated a young man from south London and gave him a dream. Thank you for this.”
In her speech, McDormand sparked the biggest applause of the night by asking every woman nominated for an award to stand up in defiance.
“I have two words to leave with you tonight, ladies and gentlemen – inclusion rider,” she said.
An “inclusion rider” is a clause that an actor can put in his or her contract, which requires a film to meet a certain level of diversity.
Dunkirk dominated the technical awards with three wins, while British cinematographer Roger Deakins won his first Oscar after being nominated 13 times.
The biggest surprise of the night was Jordan Peele’s win for best original screenplay for his racial thriller Get Out.
Peele was largely expected to go home empty-handed after winning big at the Indie Spirit Awards less than 24 hours before the Oscars.
Host Jimmy Kimmel tackled Hollywood’s sexual misconduct scandal that has led to the downfall of Harvey Weinstein and other once-powerful men in the industry.
After last year’s embarrassing best picture envelope mix-up that saw La La Land being declared winner instead of Moonlight, there were no issues with the show this time.
Warren Beatty and Faye Dunaway returned to present the best picture award after last year’s blunder.
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“As they say, presenting is lovelier the second time around,” Dunaway joked.
Kimmel ended the ceremony saying: “Well that’s how it’s supposed to go, I guess.”