His 1946 work on the "secret chromatic art" of Renaissance motets was hotly debated in its time, spurring considerable research into the issues of musica ficta and performance practice of early music.
Lowinsky studied piano, composition, and conducting in Stuttgart at the Hochschule für Musik, 1923–28.
Like many German Jews, he left the country after the NSDAP came to power; in early 1933, he moved to the Netherlands, living there for 6 years before emigrating to the United States.
He was the editor of the Monuments of Renaissance Music series from 1964 to 1977 and chaired the 1971 conference on Josquin des Prez.
Most of his published articles were collected into the massive two-volume Music in the Culture of the Renaissance (1989), edited by his second wife, musicologist Bonnie J. Blackburn.