Whitehall picked up the award for for his role in Channel 4's Fresh Meat and thanked the rest of the cast, saying that just to be working with them was "amazing".
But it was Johnny Vegas who created one of the outrageous moments of the night, by claiming some of the winners did not deserve their awards and making a dig at television stations for not commissioning fresh comedy shows.
"There are people in the room we don't think should have won," he said to the laughing audience.
"There is is stuff which has been pushed through because of finance and Channel 4 feeling like the little brother compared to the BBC."
His candid diatribe forced the show to run late, with the Channel 4 transmission ending in the middle of Steve Coogan's acceptance speech for outstanding achievement, and having dropped a recorded acceptance by Graham Norton.
Host Jonathan Ross kicked off the live show from Wembley with a barrage of quips including a risky reference to the Savile scandal.
He told the audience, which featured the cream of British comedy talent: "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."
In a wide-ranging and controversial warm-up, Ross made light of apartheid and Prime Minister David Cameron leaning in for a "selfie" photograph at the Nelson Mandela memorial service with US president Barack Obama and Danish PM Helle Thorning-Schmidt.
Paul Whitehouse collected the first award of the night as he and long-time collaborator Harry Enfield picked up the prize for Best Sketch Show for Harry & Paul. It is an award they last won in 2009.
Whitehouse said it was "a real surprise - a genuine surprise, thank you very much" before collapsing in laughter as one of his colleagues made random hand gestures and pretended to be doing sign language for the deaf, in a reference to the fake signer at the Mandela memorial.
A shocked Nina Conti picked up the Best Female TV Comic award for her show Nina Conti Live At The Apollo and said: "That is totally ridiculous."
She said she had not made a speech because everyone else in her category was so good, but thanked her family before leaving the stage.
Miranda Hart reclaimed the title of Best TV Comedy Actress title, an award she last won in 2011.
In her pre-recorded acceptance speech she jokingly plugged her upcoming tour and said "thank you to my cast and crew, although this is basically about me, this one - it is a real boost just before my tour".
Lee Mack was a double winner as Would I Lie To You, in which is is a regular with Rob Brydon and David Mitchell, was named as Best Comedy Panel Show.
He also won Best Male TV Comic. He used his acceptance speech to work Ross like a ventriloquist dummy and force him to apologise to former Fawlty Towers star Andrew Sachs for the prank phone calls he made with Russell Brand.
Mack made Ross say: "I would like to offer my resignation and give Lee Mack the opportunity to host his own chat show on ITV."
Australian comedian Adam Hills won the Best Comedy Breakthrough Artist prize.
Hills, who won for hosting Channel 4's late night satirical show The Last Leg, was in Australia where he and his wife have just had their second baby.
Whitehouse was dubbed the master of sketch comedy as he picked up the Writer's Guild of Great Britain Award to a standing ovation.
He claimed he needed to drink lots of coffee, slag off comedians and women and make calls and texts to get in the right frame of mind to write comedy, and "then I might come up with one idea and hand it over to Charlie (Higson) and Harry (Enfield), and I go home - so for me this is a false award. I can't really accept this award without thanking Harry or Charlie".
Whitehouse also dedicated his award to actor Felix Dexter, who died from cancer in October. Dexter featured in BBC comedies such as The Fast Show and Absolutely Fabulous, and acted alongside Whitehouse in the sketch show Bellamy's People.
Steve Coogan, whose creations include Alan Partridge and Paul Calf, won Outstanding Achievement award.
Whitehall was crowned as the King of Comedy in the public vote counted during the show, beating rivals including Alan Carr, David Mitchell, Graham Norton, Whitehall, Mack and Sarah Millican.
"It is an honour to win this on the same night as Paul Whitehouse, Steve Coogan and Will Ferrell - all my comedy heroes. If the Chuckle Brothers were thrown in as well it would be a clean sweep of all of my heroes," Whitehall said.
The winners at the British Comedy Awards were:
:: Best Comedy Panel Show - Would I Lie To You, BBC
:: Best Comedy Entertainment Programme - The Graham Norton Show, BBC
:: Best Sketch Show - Harry & Paul, BBC
:: Best Sitcom - Getting On, BBC
:: Best New Comedy Programme - Plebs, ITV2
:: Best Male TV Comic - Lee Mack, Would I Lie To You, BBC
:: Best Female TV Comic - Nina Conti Live At The Apollo, BBC
:: Best Comedy Entertainment Personality - Alan Carr, Alan Carr: Chatty Man, C4
:: Best Comedy Breakthrough Artist - Adam Hills, The Last Leg, C4
:: Best TV Comedy Actor - Jack Whitehall, Fresh Meat ,C4
:: Best TV Comedy Actress - Miranda Hart, Miranda, BBC
:: International Achievement - Will Ferrell
:: Outstanding Achievement - Steve Coogan
:: The Writer's Guild of Great Britain Award - Paul Whitehouse
:: The 2013 King of Comedy - Jack Whitehall
Johnny Vegas, who won Best Newcomer in 2001, unleashed his trademark rant as he presented the Writer's Guild of Great Britain Award to his sketch-writing hero Paul Whitehouse, whose credits include The Fast Show.
Speaking to an audience filled with British comedy talent and US Anchorman actor Will Ferrell, who won the International Achievement award, Vegas said: " Tonight is not about slagging off the sponsors or giving an international award away to someone just because he was here.
"Tonight is not about sitting here and saying Paul (Whitehouse) put me in the show - and I won an award about nine years ago and haven't won f****** anything since. Tonight is about what he has achieved and not me getting angry while I'm up here.
"It is not about the state of TV and the fact you won't commission anything fresh."
Having got into his stride as the crowd burst into fits of laughter, he added: "I would like to say there are people in this room that we don't admire. There are people in the room we don't think should have won. "There is stuff which has been pushed through because of finance and Channel 4 feeling like the little brother compared to the BBC, but tonight is about Paul Whitehouse."
He rounded off with a "genuine moment of sincerity" - describing Whitehouse as the "godfather" of comedy.
"Paul's comedy compared to other people," he said - muttering "The Office" under his breath - "does not make victims of anything and it does not claim that it is getting over boundaries."
To applause, he added: "Paul Whitehouse finds the joy and beauty in life, in people that you would not notice."
The Office has been a worldwide hit for Ricky Gervais.