The shows took home three prizes each at Sunday night's ceremony in London, which was hosted by Alan Davies.
Sherlock co-creator Steven Moffat won the 'Writer' award for the episode 'A Scandal in Belgravia', and the same episode also triumphed in the 'Editing: Fiction' and 'Sound: Fiction' categories.
David Attenborough's documentary series Frozen Planet was presented with the 'Editing: Factual', 'Photography: Factual' and 'Sound: Factual' awards for its first episode 'To the Ends of the Earth'.
Great Expectations, which starred Douglas Booth and Gillian Anderson, was named the winner in the 'Production Design', 'Photography and Lighting: Fiction' and 'Visual Effects' categories.
Hugo Blick was honoured with his first BAFTA in the 'Director: Fiction' field for his work on BBC Two's crime thriller The Shadow Line, while Brian Eno also won his first BAFTA in the 'Original Music' category for Channel 4 drama Top Boy.
Birdsong, The Cube, Educating Essex and The X Factor were also presented with technical awards, and colourist Aidan Farrell was honoured with the Special Award for his achievements in the post-production industry.
Appropriate Adult, Sherlock and This is England '88 lead the nominees at the Arqiva British Academy Television Awards, which take place on Sunday, May 27.
Watch a trailer for Sherlock's 'A Scandal in Belgravia' below: