The scheme saw off challenges from five other shortlisted projects, including a community health centre in Partick by Gareth Hoskins Architects, to claim the £25,000 prize - the most valuable award in British architecture.
The controversial Holyrood development was officially named the Best Building in Scotland 2005 at a ceremony in Edinburgh today (5 October).
This announcement sets up a possible double whammy of big wins for the Scottish Parliament, which is also shortlisted for the RIBA Stirling Prize.
Speaking about the award which, ironically, is supported by the Scottish executive,
RIAS President and chair of the judging panel, Douglas Read, said: 'Here is a building shrouded in controversy, one which provokes strong reactions from everyone.
'The jury was fully aware of all this and we had determined that we were there to judge it as architecture - not as scandal.'
He added: 'Enric Miralles' concept of stopping the Old Town with the strong North/South MSPs office block and then setting up a campus parliament to the east of it has resulted in one of the most instantly identifiable buildings in Europe.
'There is no part of this building that has not been consciously designed, everything has been considered.
'It also has complete public access and a dedication to transparent democracy and, while meeting all these demands, it also takes full advantage of its prominent site to merge in with the land - as Miralles always said he wanted it to. It is a magnificent achievement and the design team EMBT/RMJM deserves our fullest congratulations.'
This year's other judges were David Porter, head of Mackintosh School of Architecture, Glasgow, Kathryn Findlay, director of Ushida Findlay Architects, and Anthony Reddy, president of the Royal Institute of the Architects of Ireland.
Previous winners of the award include the An Turas Tiree ferry stop, by Sutherland Hussey Architects with Jake Harvey, and the St Aloysius College Clavius Building, designed by Elder and Cannon Architects.