The programme's executive producer Steven Moffat collected the award on behalf of the long-running sci-fi series, which will soon see Matt Smith hand over to Peter Capaldi in the lead role as The Doctor.
Smith's predecessor, David Tennant, also took a prize at last night's event at London's Dorchester Hotel, collecting the best actor trophy, which was one of two prizes for ITV police mystery Broadchurch. It also took the best new drama prize.
Coronation Street took the keenly fought best soap award, and the show also landed the best soap actress prize with Michelle Keegan collecting the title for her role as Tina McIntyre.
BBC1 rival EastEnders also enjoyed its share of wins with Shane Richie named best soap actor for playing Alfie Moon. His co-star David Witts, who plays brooding Joey Branning, was also honoured as best soap newcomer.
Richie dismissed the notion that there was any competitive edge between the soaps when it comes to collecting prizes.
"We've got friends in a lot of the shows that are here tonight and I look forward to catching up with them," he said.
"They have the same schedules, the same worries, they've got bills to pay and whoever wins tonight, people won't remember next week."
Miranda Hart was rewarded for her role in BBC1 drama Call The Midwife with the best actress prize for a second year, and Mrs Brown's Boys retained its title as best comedy.
Britain's Got Talent was crowned Best Talent Show. Judge Amanda Holden told reporters she had been quick to congratulate her boss Simon Cowell after hearing he was expecting a baby with lover Lauren Silverman.
Asked what sort of father Cowell would make, Holden said: "I think he is going to be brilliant and I don't think he is going to be a disciplinarian. I think he will have an unruly, naughty boy - just like himself."
Ant and Dec were triple winners at the awards as they collected a trio of gongs for their shows.
The duo landed prizes for best reality show for I'm A Celebrity ... Get Me Out Of Here!, best talent show for Britain's Got Talent, and best entertainment show for Ant & Dec's Saturday Night Takeaway.
Best daytime programme went to The Jeremy Kyle Show for the third year running.
Winners at the ceremony - officially called the TVChoice Awards 2013, in association with Daz - were voted by viewers and readers of the magazine.
Full list of winners and presenters:
:: Best Soap - Coronation Street
:: Best New Drama - Broadchurch
:: Best Drama Series - Doctor Who
:: Outstanding Contribution Award - Doctor Who
:: Best Actor - David Tennant, Broadchurch
:: Best Actress - Miranda Hart, Call the Midwife
:: Best Comedy - Mrs Brown's Boys
:: Best Reality Show - I'm A Celebrity ... Get Me Out Of Here!
:: Best Talent Show - Britain's Got Talent
:: Best Entertainment Show - Ant & Dec's Saturday Night Takeaway
:: Best Factual Entertainment & Lifestyle Show - Paul O'Grady: For The Love Of Dogs
:: Best Daytime Show - The Jeremy Kyle Show
:: Best Food Show - Jamie's 15 Minute Meals
:: Best International Show - The Big Bang Theory
:: Best Soap Actor - Shane Richie (Alfie Moon, EastEnders)
:: Best Soap Newcomer - David Witts (Joey Branning, EastEnders)
:: Best Soap Actress - Michelle Keegan (Tina McIntyre, Coronation Street)