Made from steel and glass, the untitled work, which resembles vines or a screen of hanging vegetation, will be completed by the end of this week.
Boyce, who studied at the GSA and won the Turner Prize in 2011, said he thought the new building - which is open to students whilst still being built - was "amazing".
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It was designed by US architect Steven Holl in partnership with Glasgow-based JM Architects.
Holl met Boyce in New York when the plans for the building were in their early stages and Boyce thinks the site is an "incredible building, the kind which Glasgow has not seen before".
Steven Holl Architects' design for the new building envisaged a glass artwork integrated into the entrance.
It was designed so it would relate to Charles Rennie Mackintosh's use of glass in the original 1910 Art School.
The art work, Boyce's second permanent art work, is made from a 4.3m x 8.9m hanging screen of steel and glass geometric vines.
There are 19 vines in total with 122 glass panels with four different colours
Each vertical line sprouts a number of horizontal branches which support the glass 'leaves' and there are four different sizes of glass leaf in different colours.
Holl said: "Marking the entrance of our new building at the Glasgow School of Art is a flourish of coloured glass catching and projecting washes of coloured light by Martin Boyce.
"We see this colour in positive contrast to the original colours of Mackintosh and an inspiration to students and the community."
The creation of the artwork was backed by a grant from Creative Scotland.
Boyce, who has a major new show at the Sydney Biennale coming up in March, plus significant architectural works being planned in Zurich and Vancouver, said he was delighted to be asked to contribute to the new building.
He said: " I think the building is brilliant, and I think people will have a new relationship to it once they step inside. From the outside, it almost looks like an [architect's] model or maquette but its complexity and its light is revealed once you are inside."
"We are delighted that Steven Holl Architects should have selected one of our alumni to create the signature artwork for the Reid Building design," said Professor Tom Inns, director of the Glasgow School of Art.
"Architecture and nature are two major themes in Martin's practice and these are brought together seamlessly in this beautiful new work."