Whitehall picked up the best TV comedy actor award for his role in Channel 4's Fresh Meat, and also collected the king of comedy prize voted for by viewers during the televised show.
As he was awarded his second gong he was joined on stage by his grumbling father Michael, a talent agent and TV sidekick, who berated host Jonathan Ross for insulting him from the stage earlier in the event.
Other winners at the show included Miranda Hart who was named best TV comedy actress, and Paul Whitehouse picked up an honorary prize for his contribution to comedy writing.
But the event was derailed by a rambling introduction from comic Johnny Vegas as he handed over Whitehouse's prize, and his lengthy contribution meant lifetime achievement award recipient Steve Coogan was cut off just moments before he launched into his speech.
Coogan was showered with confetti and the credits ran just as he was getting into his stride.
As ever, the awards included near-the-knuckle jokes and bad language from Lee Mack and Whitehouse.
Jonathan Ross kicked off the live show from Wembley with a barrage of quips including a risky reference to the Savile scandal. He said: "They have demolished Television Centre. The studios we have all known and loved. It is now a building site and ironically it is now a far less dangerous place for children to play than ever before."
But it was Vegas who created one of the outrageous moments at the ceremony, by claiming some of the winners did not deserve their awards, criticism of the sponsor and making a dig at television stations for not commissioning fresh comedy shows.
In addition to his honorary prize, Whitehouse also collected best sketch show award for Harry & Paul, which he and Harry Enfield last won in 2009.
He headed to the stage with a pal who made random hand gestures and pretended to be doing sign language for the deaf, in a reference to the fake signer at the Nelson Mandela memorial service.