And political satire The Thick Of It also scooped two awards, including Best Comedy Performance for Chris Langham, while The Apprentice was named Best Feature.
By contrast, ITV1 came away with just one prize – Best Entertainment Programme for The X-Factor.
Deal Or No Deal host Noel Edmonds missed out on his first Bafta. He had been hoping to cap his career comeback by winning Best Entertainment Performance. But instead the award went to Jonathan Ross for his Friday night chat show.
Jamie Oliver’s crusade to improve school dinners earned him an outstanding presenter award and his Channel 4 series won Best Factual Series.
Davina McCall hosted the glittering ceremony from the Grosvenor House Hotel in central London.
Doctor Who stars Billie Piper and David Tennant were there to collect their two awards – Best Drama Series and the Pioneer Audience Award (voted by viewers). Piper, who was accompanied on stage by a Dalek, refused to reveal whether her character Rose was soon to be killed off. “You’re just going to have to wait and see,” she smiled.
Russell T Davies, creator of the new series of Doctor Who, said the success of the sci-fi show proved viewers still wanted family entertainment.
“We were told that bringing it back would be impossible, but we did it,” he said.
The BBC1 adaptation of Charles Dickens classic Bleak House won the award for Best Drama Serial, while Anna Maxwell Martin was named Best Actress, beating co-star Gillian Anderson.
Sir Alan Sugar broke into a rare smile when The Apprentice beat Dragon’s Den, Ramsay’s Kitchen Nightmares and Top Gear to win Best Feature.
The Amstrad tycoon was keeping tight-lipped about which of the two finalists - Ruth Badger or Michelle Dewberry – would emerge as winner of series two.
“They have got different abilities – one is a bull in a china shop and the other is a very deep thinker. But you get all different types of people in business,” he said.
BBC4 satire The Thick Of It won Best Sitcom and Best Comedy Performance for Langham.
Another Langham show, BBC2’s Help, won Best Comedy Programme.
In December Langham was arrested in connection with a police investigation into internet child pornography. No charges have been brought and he is currently on bail.
Edmonds could not hide his disappointment at failing to land a Bafta. Winner Jonathan Ross joked Edmonds was enjoying “the most surprising comeback since the BNP”.
Backstage, Ross said he thought Edmonds should have won.
“Noel does a tremendous job on Deal Or No Deal. It’s a brilliant format but what really makes it so watchable and so entertaining is Noel’s presence. I kind of wish he won, which probably makes it worse for him,” he said.