The Ubisoft squad-based shooter title, released in March 2006, also won the award for Technical Achievement.
Ghost Recon, available on Xbox 360 and PC platforms, was hailed on launch for its fast-paced tactical gameplay which can be undertaken in three modes: single-player campaign; squad-based multiplayer; and competitive multiplayer.
Other award winners notching up two Bafta trophies apiece were LocoRoco, Lego Star Wars II: The Original Trilogy and Shadow of the Colossus.
Sony PlayStation title LocoRoco won the award for best game for young persons and best character, seeing off Han Solo, Lara Croft, Agent 47 and Rogue Trooper in the latter category.
The Game of the Year award was sponsored by PC World.
- Full list of the 2006 video games Bafta nominees and winners