The interactive work on Walking with Beasts won the enhancement of linear media award. The series, which is the sequel to Walking with Dinosaurs, will be broadcast in mid-November and will be the UK's first interactive documentary broadcast on all digital platforms.
Digital satellite viewers will be able to choose different narration soundtracks or watch extra video streams with background information on the programme. Digital viewers will also have access to enhanced text services such as fact files and message boards on the beasts.
For the enhancement award the BBC beat off competition from Disney for Snow White and the Seven Dwarfs and ITV's Who Wants to be a Millionaire.
The panel of judges said, "This is a ground breaking, inspirational work."
Ashley Highfield, Director of BBC New Media said, "To win an award for a service that hasn't even been broadcast yet is a real tribute to the ground-breaking work that teams across the BBC have been doing."
The BBC news website was awarded the Best News Website award for the fourth year running, beating CNN Europe and ITN Online.
Mike Smartt, the editor in chief of New Media said, "To win a fourth Bafta in four years is a great tribute to our team of designers, developers, producers, technicians and journalists, all of whom work so hard to innovate and improve the site."