BBC director of television Jana Bennett said that the win was testament to the quality of the output produced by the corporation.
"Having a tribute like this from the industry is a fantastic testament to the quality of the creative work, not only on BBC Two in its 40th year, but also on BBC Four, one of our youngest channels.
"Day after day, they deliver excellent programmes across all genres, which are both prized and valued by the audiences."
BBC Two was praised by the judges for its commitment to talent and doing an "amazing public service job" with high-profile documentaries such as 'Horizon' and 'Battlefield Britain'.
They described BBC Four, the channel behind 'The Alan Clark Diaries' as the channel they most wanted in their home.
Sky News, LivingTV, BBC Three, BBC Four, ITV2 and Sky One had been shortlisted for the satellite category in the Channel of the Year. BBC One, BBC Two, ITV, Channel 4 and Five were shortlisted for Terrestrial Channel of the Year.
The ceremony was hosted by comedian Bob Mortimer at the festival on Saturday.
Judges included 'I'm a Celebrity...' star Rhona Cameron, Heat's Boyd Hilton and comedian Catherine Tate, as well as Guardian reporter Janine Gibson and 'The Bill' actress Josie D'Arby.
The Channel of the Year Awards are now in their third year. Five won the first trophy in 2002, followed by BBC Two last year.
MTV was named non-terrestrial channel of the year in 2003 after Sky News won that accolade in 2002.
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