More from: Rogers' lands prized Lyon airport project
The practice saw off competition from the bookies' favourite - Zaha's Hadid's Phaeno Science Centre in Germany - to scoop the award.
The other projects up for the £20,000 prize were Caruso St John's Brick House, David Adjaye's Idea Store, Hopkins' Evelina Children's Hospital and the Welsh Assembly building, also by Rogers.
The judges said of Barajas: 'Whatever the means of approach, by air or by land, the sheer scale and complexity of what has been tackled and achieved here cannot be over-estimated.
'In response to the key challenge: that of efficiently processing constantly changing passenger flows and associated luggage handling, the resulting building presents a straightforward linear diagram in the form of a clear sequence of spectacular spaces for both departing and arriving passengers.'
Two of the RIBA's Special Awards were also announced on the night.
Knox Bhavan's Holly Barn won the Manser Medal, sponsored by The Architects' Journal, for the best one-off house designed by an architect in the UK.
And Alison Brooks Architects' Wrap House won the Stephen Lawrence Prize, sponsored by the Marco Goldschmied Foundation, for the best example of a building with a construction budget of less than £1 million.
For more extensive coverage of the evening, including an interview with the winning team, pictures of the night and a series of immediate reactions from the crowd, visit www.ajplus.co.uk/riba2006.