Prelog was elected to the American Academy of Arts and Sciences in 1960 and the United States National Academy of Sciences in 1961.
Prelog was elected a Foreign Member of the Royal Society (ForMemRS) in 1962 for his contribution to the development of modern stereochemistry.
Prelog received the 1975 Nobel Prize in Chemistry for his research into the stereochemistry of organic molecules and reaction, sharing it with the Australian/British research chemist John Cornforth. He was elected to the American Philosophical Society the following year.
In 1986, he became an honorary member of the Yugoslav Academy of Sciences and Arts. Prelog was also a member of Serbian Academy of Sciences and Arts.