The 13-part, £10m series was crowned most popular drama at the award ceremony at the Royal Albert Hall in London, which is voted for by viewers.
It saw off competition from Desperate Housewives, The Bill and the ITV prison drama Bad Girls.
Christopher Eccleston, who played the Time Lord, was named best actor. Billie Piper, who played his assistant Rose Tyler, won best actress.
The series, written by Russell T Davies, kept many elements familiar to fans of Doctor Who, including the Tardis and the Daleks, but was reinvented for a new generation.
Nearly 13 million people tuned into the first episode - the biggest audience since Tom Baker's heyday in the 1970s. Within days of the start of the first series, however, Eccleston quit, saying that he did not want to be "typecast". A Christmas special, a second series and a spin-off are in the offing.
Jamie Oliver's School Dinners, the Channel 4 show which highlighted funding problems in school dinners, was named most popular factual programme.
Oliver, who took a petition to the Government urging it to improve school dinners, was given a special recognition award.
Little Britain was named best comedy programme over The Simpsons, Will and Grace and Max and Paddy's Road To Nowhere. Sharon Osbourne, one of the judges on ITV's The X-Factor, was named most popular expert on TV, a new category. The X-Factor also won best entertainment programme.
Tony Warren, the creator of Coronation Street, was presented with a TV Landmark award.Reuse content