The premises will also temporarily house Audi's sales operation while the nearby existing showroom is demolished and rebuilt as a two-storey used car display.
The new after sales building, designed by SDA Architects in Leeds, features a 20 bay workshop, large valeting department and compound facility.
Its completion means that work can now begin on redeveloping the original dealership into a 17 car showroom featuring a two storey external used car display area capable of displaying 60 cars and meeting the new corporate design guidelines of Audi.
Mark Taylor, group property director at JCT600, said: "The completion of phase one on schedule means that customers can already benefit from improved aftersales facilities at Clifton Moor which will also serve as our sales facility while we build our dedicated sales development."
The new showroom will incorporate Audi's latest architecture featuring perforated and anodized aluminum sheets. Work on site is now underway with construction due to be completed by the end of the year.
The investment in York Audi, which JCT600 acquired three years ago, is part of a £10m redevelopment programme being undertaken by the Bradford-headquartered motor retailer this year.
In March, JCT600 acquired £200m-turnover Gilder Group from its outgoing chief executive Garry Scotting. The deal is the largest in its history and takes revenues beyond the £850m mark.