The star dropped the F-bomb as she made a speech to accept the Best Drama gong for Killing Eve.
Phoebe, who created and wrote the first series of the hit series, shouted “fuck!” as she appeared on stage with many of the show’s cast and crew.
However, BBC bosses bleeped out her swearing, despite airing well after the 9pm watershed.
The ceremony was broadcast from London’s Festival Hall on a 75-minute delay, meaning producers had made a considered choice to cut Phoebe’s f-bomb from going out to BBC One viewers.
During her speech, she went on to praise her “charismatic, breathtaking, energetic” team.
“I can’t speak it’s so unbelievably exciting,” she said.“Thanks for everyone for taking risks. Jodie Comer almost swallowed a wasp in Tuscany. It was a really edgy moment that we did capture on camera.”
Killing Eve was the big winner on Sunday night, taking home three awards in total.
Other prizes were given to Jodie Comer for Best Actress for her role as Russian assassin Villanelle, while Fiona Shaw, who plays MI6 agent Carolyn Martens, was awarded Best Supporting Actress.
Bafta previously revealed it had bent the rules to include Killing Eve in this year’s nominations, as usually they require nominees to have had “worldwide premiere transmission in the UK” – which Killing Eve did not.
The show - a BBC America production - aired in the US six months before it was shown here, but bosses allowed it to be included “owing to the significant creative contribution from key talent residing in the UK both in front of and behind the camera.”
Phoebe Waller-Bridge appeared on stage earlier in the evening to hand out an award, reuniting her with Fleabag co-star Andrew Scott, aka The Priest - serving up one of the moments of the night.