The QI star is known for poking fun at Hollywood stars during the annual ceremony but a gag he made about winning costume designer Jenny Beavan was a step too far for some viewers.
After Jenny picked up the trophy for her work on Mad Max: Fury Road, host Stephen remarked: "Only one of the great cinematic costume designers would come to an awards ceremony dressed as a bag lady."
The joke came under fire from viewers, prompting Stephen to tweet: "Will all you sanctimonious f**kers f*ck the f*ck off Jenny Beavan is a friend and joshing is legitimate. Christ I want to leave the planet."
He also shared a photo of himself and Jenny after the show, showing she was holding no hard feelings towards him.
But Stephen now appears to have deleted his entire Twitter account.
He has hosted the British Academy of Film and Television Arts awards for 11 years. It's not been announced yet whether he will return for the 2017 ceremony.
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