Sauer studied chemistry from 1967 to 1972 at the Humboldt University of Berlin and was awarded a doctorate in chemistry in 1974. He continued to do research there until 1977, when he joined the Academy of Sciences, Central Institute of Physical Chemistry in Berlin, one of the leading scientific institutes of the former GDR (East Germany).
For a brief time during and after the German reunification (1990–1991) he was the deputy technical director (catalysis and sorption) for BIOSYM Technologies in San Diego, California (now BIOVIA). He remained an advisor for BIOSYM until 2002.
In 1992, he joined the Max Planck Society as head of the Quantum Chemistry Group in Berlin. In 1993, he became full professor of physical and theoretical chemistry at the Humboldt University of Berlin. He retired from his chair in October 2017 and was succeeded by Martin Schütz, who died the following year. Sauer remains affiliated with the university as a senior research fellow.
He is an active research scientist in quantum chemistry and computational chemistry. His computational studies have allowed for a better understanding of the structures and activities of some catalysts such as zeolites, specifically their acid sites,  as well as the interpretation of solid state NMR spectra of nucleus Si-29, and quadrupolar nuclei such as Na-23,  Al-27 and O-17.