The Award for Outstanding Visual Effects, in the Special, Visual & Graphic Effects category, went to the BBC's Doctor Who episode Deep Breath
Runners up were Vine FX for Atlantis, Colossus Productions, Vision3 and Zoo VFX for David Attenborough's Conquest of the Skies 3D, and Screen Scene for work on Ripper Street.
Milk won the award alongside BBC Wales VFX and special effects companies Millennium FX and Real SFX, who created the practical effects for the episode.
The focus of Milk's work on Deep Breath was creating the sinister 'Half-Face Man' character.
As Digital Arts revealed back in August, Milk replaced one entire side of actor Peter Ferdinando's head in one of its 117 digital shots for the episode.
Milk created a CG hollow cage-like structure for the missing half of character's head, as well as the visible internal workings of his head which resemble the mechanics of a clock, with moving cogs, pistons and rotating mechanical parts.
MilK also won this same award last year for its VFX work on the Doctor Who: 50th anniversary special episode: Day of the Doctor.
CEO Will Cohen said Milk was honoured to be recognised by the Academy for its work on the show for the second year in a row, adding "for a company set to celebrate its second year in business at the beginning of June this is another fairytale ending to the year for Milk!"
"It is a privilege to work with Stephen Moffat and the BBC Wales team on Doctor Who and provides us with an opportunity as VFX artists to help push the boundaries of what can be done visually on television."
The British-American horror series Penny Dreadful was the biggest winner of the BAFTA ceremony, scooping three awards for Original Music, Production Design and Make Up and Hair Design.
Other winners on the night included BBC dramas Sherlock, which received two awards and Marvellous, which picked up one award.