The building, designed by Steven Holl Architects of New York and Scottish-based JM Architects, triumphed at the prestigious AJ100 awards run by the Architect's Journal in London last night.
The glass-clad edifice opposite Charles Rennie Mackintosh's world-famous art school building was named building of the year.
It beat high-profile projects such as the Queen Alia International Airport in Amman in Jordan, designed by Foster and Partners, and the 29-storey Al Bahr Towers in Abu Dhabi, designed by Aedas.
The annual AJ100 celebrates the UK's top 100 architectural practices. The Seona Reid Building has not been universally praised by architecture critics but was the award judges' unanimous choice.
The exterior of the building is coated in glass, while its interior is architecturally dominated by three huge concrete tubes - "driven voids of light" - which have been designed to light and ventilate students' design studios.
The jury said it wanted to make special mention of the role played by Glasgow-based JM Architects alongside Stephen Holl in making this "bold, complex building" .
"The role of executive and associate architects in the creation of good and great buildings should be more fairly acknowledged," it said. "The AJ and its jury for this award category is proud to take this lead."
Judge Mary Duggan of Duggan Morris Architects said: "The rhetoric of education buildings has been recast. It offers fresh insights into what is possible."
Hanif Kara, design director and co-founder of the AKT II structural engineering firm, said the building has a "vitality that transcends the image", while Ms Duggan admired its "clever choreography of connecting spaces".
The AJ's review of the building said: "It takes risks - more than the past three Stirling Prize winners put together - and, while not all of them succeed, it's the effort that counts. The Reid Building matters because it dares to walk the plank.
"In this respect, it works as art."
Previous winners of the Building of the Year prize include John McAslan and Partners King's Cross Station, and Stanton Williams' Central St Martins. The Reid building was officially opened in April, but opened to students in January.
At that time Steven Holl himself said: "We had a lot of controversy, there were suspect articles from people second-guessing what this building could be, and I am very excited people can come inside of it. You must come in, walk the space, and that is really when you feel the space and the energy.
"I think the students 100% get it, and I think the people who have been in it get it, but I would like to see those early critics come inside."