After she collected the award, awards host Fry quipped: "Only one of the great cinematic costume designers would come to an awards dressed as a bag lady."
The dig drew mixed reactions from the audience, with some booing.
But Fry tweeted: "So just a word to the tragic figures who think calling Jenny Beavan a bag lady was an insult. She's a dear friend and she got it. Derrr."
He added: "Will all you sanctimonious f****** f*** the f*** off Jenny Beavan is a friend and joshing is legitimate.
"Christ I want to leave the planet."
He said they had worked together on Gosford Park and Sherlock Holmes: Game of Shadows.
Beavan accepted the awards with the words: "I live, I die, I live again", before praising the directors she had worked with throughout her career.
Fry later tweeted a picture of himself with his arm around Beavan.
He wrote: "Jenny Baglady Beavan and Stephen Outrageous Misogynist Swine Fry at the #EEBAFTAs after party."
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