Currently the world's second tallest building, the skyscraper was awarded Architectural Design of the Year during a ceremony at the Cooper Hewitt Smithsonian Design Museum in New York last week.
A campus for students in Melbourne took home the Interior Design of the Year prize, while Landscape Architecture of the Year went to a water re-use project at a Sydney park.
More awards were also given out to projects worldwide as part of the 2016 American Architecture Prize (AAP).
"The AAP jury has selected exceptional designs in over 40 categories across the disciplines of architecture, interior design, and landscape architecture," said a statement from the awards organisers.
"Each design was evaluated on its own merit based on characteristics of form, function, and innovation."
The design of the Shanghai Tower, which completed in January 2016, was led by architect Dan Winey of Gensler.
Its curved and twisted form was generated through a series of wind-tunnel tests, and contains 121 storeys that are divided into nine vertical zones.
Shops are located at the base, offices in the centre, and hotels, cultural facilities and observation decks at the top.
Interior winner, The Infinity Centre at Melbourne's Penleigh and Essendon Grammar School, was created by Australian firm McBride Charles Ryan for senior students.
The building is shaped like an infinity symbol, and features a library in the space where the wings cross.
Internal spaces for a variety of functions and departments are distinguished through different materials and colours.
Also in Australia, the Sydney Park Water Re-use Project is described as the city's largest environmental project to date.
It involved transforming 44 hectares of post-industrial land into a wetlands park, which captures and cleans water for distribution across the urban area.
Landscape architects Turf Design Studio & Environmental Partnership worked with water experts Alluvium, artists Turpin + Crawford Studio, ecologists Dragonfly Environmental and engineers Partridge to complete the project.
The American Architecture Prize was set up as an annual awards programme this year, with the aim to "advance the appreciation of quality architectural design worldwide".