The ITV1 soap won the 'Best Soap or Continuing Drama' award ahead of last year's winner EastEnders.
Sherlock's Andrew Scott beat his co-star Martin Freeman to win 'Best Supporting Actor' for his role of the villainous Moriarty.
Benedict Cumberbatch was beaten to the 'Best Actor' prize by Dominic West for playing Fred West in Appropriate Adult.
West's co-star Emily Watson also won 'Best Actress' award as Janet Leach in the ITV drama.
Talking about her role, Watson said: "It was such a disturbing place to go. In my speech I was very overwhelmed I forgot to thank Janet Leach, she gave very generously to us.
"The public perception of the West case is a tabloid-driven view and then I read the script and it was a very intelligent piece full of integrity. It's a deep abyss right in the middle of our society."
> BAFTA Television Awards 2012: The winners in full
Appropriate Adult lost out to Shane Meadows's This Is England 88 in the 'Best Mini-Series' category.
Rolf Harris was awarded with a BAFTA Fellowship recognising his "outstanding and exceptional contribution to television", while Doctor Who's Stephen Moffat received a Special BAFTA for "outstanding creative writing contribution to television".
Harris told BBC News: "It's unbelievable for a start, it's very humbling and thrilling. I can't tell you how exciting it was when they asked if I would accept the award."
Meanwhile, The Young Apprentice won 'Best Reality and Constructed Factual', while viewers voted for Celebrity Juice to win the 'Audience Award'.
Graham Norton, Jennifer Saunders and Stewart Lee's Comedy Vehicle were also among the winners.