It was supposed to be "A Star is Born's" night.
The big win was preceded by Rami Malek winning Best Actor - Drama for his performance as Mercury. Green Book is a true story about a budding friendship between an African-American pianist and a white bouncer on a tour of the Deep South in the early 1960s.
The former Batman played former US Vice President Dick Cheney in Vice.
"Green Book's" director, Peter Farrelly, made a plea for tolerance in his acceptance speech.
"It's not something I really wish to talk about tonight", said producer Graham King. "We need to understand how much we have in common".
Bohemian Rhapsody will be available to own on February 12, 2019.
There can be 100 people on the Golden Globes red carpet, but it only takes two to lift the train of Lady Gaga's dress. Needless to say, if there is one person who could do it, it is Gaga. Twitterati is hugely disappointed with the fact that these two films won the Best Film for Drama and Comedy category. The critically praised show, which just wrapped its sixth and final season, stars real-life couple Keri Russell and Matthew Rhys.
She and Cooper lost in their respective acting categories.
"The Americans" beat out "Homecoming", the new Julia Roberts show about a counselor at a mysterious treatment center for returning veterans, and "Killing Eve", about the treacherous rivalry between two risky women, a British intelligence officer and an assassin.More news: China and United States to hold trade talks in Beijing
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Co-host Sandra Oh, who was born in Canada of Asian descent, paid tribute to the slew of Golden Globe-nominated films and TV shows featuring black and Asian actors and directors, including "Crazy Rich Asians", "Black Panther", and "BlacKkKlansman".
Bradley Cooper - who plays the aging rocker opposite Gaga's singer in Star - had been favourite for best actor in a drama but was edged out by Malek.
There were deserved wins for Mahershala Ali for Green Book, a true story of race in America in the 1960s, and that film was the night's biggest victor. Attention fame monsters: Can we give it up for Lady Gaga?
And Glenn Close urged women to stand up and take credit, like her character in The Wife eventually does. "We have to find personal fulfillment", the 71-year-old actress said.
Malek thanked Queen members Brian May and Roger Taylor, as well as Mercury for providing the role of a lifetime.
British actress Olivia Coleman was a victor for bawdy historical romp "The Favourite".
Mahersala Ali won for his supporting role in the film "Green Book" and the film also won the best screenplay prize.
There are also the Comedy/Musical films to consider for Oscar competition.