The star won the supporting actress award for her role as the mother of a murdered son in Accused (Mo's Story) and picked up her second Bafta for female in a comedy for her role in Olympic satire Twenty Twelve.
She beat three other actresses including her Twenty Twelve co-star Jessica Hynes to the award, saying: "I'm not even the funniest one in our own programme".
Speaking backstage, Colman said she was "thinking there has been a mistake" after winning her second award.
She joked: "I'm a bit doomed now, I'm never going to work again" and said her appeal was down to people thinking she was "safe", saying: "I'm never going to take anyone's husband".
She said Hollywood had not come calling, but said she would be happy to go if it did adding: "Of course, it's warm and I think they pay better".
Host Graham Norton introduced the show, formally known as the Arqiva British Academy Television Awards, from the Royal Festival Hall in London.
He kicked off with a series of gags about the spate of recent celebrity arrests, saying the show had to start before "any of our presenters or guests are unavoidably detained" before Homeland stars Damian Lewis and David gave the evening's first award - for best drama series - to Last Tango in Halifax.
The show, about a pair of pensioners who rekindle a romance late in life, beat off competition including ITV cop show Scott and Bailey.
One of its stars, Anne Reid said it was the "most fantastic series to be a part of" and added: "I am so happy the BBC has decided to do love stories about people who are over 35 because some of us do have quite interesting lives when we get to 70".
Sheridan Smith was named leading actress for her role in Mrs Biggs.
A tearful Smith, who played the wife of Great Train Robber Ronnie Biggs in the ITV show, said: "Is this a wind-up? Is this for real?"
The Bafta for leading actor went to Ben Whishaw for Richard II (The Hollow Crown).
The award for sport and live event was won by Channel's 4's coverage of the 2012 Paralympics.
One of the presenters, Ade Adepitan, said the win was "an absolute honour".
He said: "Thank you Channel 4, for letting us be ourselves."
Shameless star Anne Marie Duff announced the award for supporting actor went to Shakespearean veteran Simon Russell Beale for his performance as Falstaff in the BBC version of Henry IV Part 2.
Olympic satire Twenty Twelve won the sitcom award.
The award for entertainment programme went to Norton's chatshow with the Irish comic accepting his own award before returning to hosting duties.
He joked: "It's funny how that can cheer an evening up."
The award for reality and constructed factual show went Made in Chelsea.
One of its stars, Francis Boulle said: "Who would have thought you would get a Bafta for being posh?"
There was a special award for sports presenter Claire Balding who hosted much of the Olympics coverage.
The tearful star said the games brought an "incredible positive energy, a feeling we could do anything and we did".
The features award went to The Great British Bake Off with co-host Mel Giedroyc saying: "Who knew there could be so much drama in a scone? Amazing."
EastEnders won the award for soap and continuing drama and the award for male in a comedy went to Steve Coogan for Welcome To The Places Of My Life.
The Revolution Will Be Televised was named the best comedy programme.
The Radio Times Audience Award, voted for by viewers, went to Sky's bloodthirsty fantasy series Game of Thrones.
All In The Best Possible Taste with Grayson Perry, which saw the cross-dressing potter travel the country to see what different people considered tasteful, won the award for specialist factual.
The international award went to US show Girls, with the award for entertainment performance going to Alan Carr for his chatshow.
Accepting his award, he said: "I'm going to kill the person who selects the clips because it is normally funny".
Monty Python star Terry Jones presented his co-star Michael Palin with the Bafta Fellowship.
Accepting his award to a standing ovation, Palin said his first celebrity invite was to open some public toilets in Lambeth and said it had been "quite a journey" from there to the Royal Festival Hall.
He said his award was for "thoroughly enjoying myself for the last 48 years and I feel slightly guilty about that".
The award for factual series went to BBC Three's Our War which followed events on the frontline in Afghanistan from the perspective of the troops on the ground.
This World's investigation into child abuse in the Catholic church won the award for current affairs, beating ITV's documentary about Jimmy Savile's sex crimes, a Panorama special on the crisis in Britain's housing and Al Jazeera's investigation into the death of Yasser Arafat.
The award for news coverage went to Granada Reports programme, Hillsborough - The truth at last.
BBC Two's Murder was named the best single drama, while 7/7: One Day In London won the award for single documentary.
The BBC's adaptation of John Braine's novel Room at the Top, which starred Doctor Who's Jenna-Louise Coleman, won the award for mini-series.
Ben Whishaw - Richard II (The Hollow Crown)
Sheridan Smith - Mrs Biggs
Simon Russell Beale - Henry IV Part 2(The Hollow Crown)
Olivia Colman - Accused (Mo's Story)
Female Performance in a Comedy Programme
Olivia Colman for Twenty Twelve
Male Performance in a Comedy Programme
Steve Coogan for Welcome To The Places Of My Life
Room At The Top
Last Tango In Halifax
Soap and Continuing Drama
All In The Best Possible Taste with Grayson Perry
7/7: One Day In London
The Great British Bake Off
Reality and Constructed Factual
Made In Chelsea
The Shame Of The Catholic Church (This World)
Hillsborough - The Truth At Last (Granada Reports)
Sport and Live Event
The London 2012 Paralympic Games
The Graham Norton Show
The Revolution Will Be Televised
Radio Times Audience Award (voted for by members of the public)
Game of Thrones
Alan Carr - Alan Carr: Chatty Man
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