Lowinsky studied piano, composition, and conducting in Stuttgart at the Hochschule für Musik, 1923-28. In 1933, he obtained his Ph.D. from the University of Heidelberg, studying under Heinrich Besseler. His dissertation was on Orlando di Lasso. He lived in the Netherlands from 1933 to 1939, and in 1940 emigrated to the United States. In 1947 he became a United States citizen. He taught at Black Mountain College (1942-47), Queens College, New York (1947-56), and the University of California, Berkeley (1956-61). From 1961 he taught at the University of Chicago. He was the editor of the Monuments of Renaissance Music series from 1964 to 1977, and chaired the 1971 conference on Josquin des Prez.
Lowinsky was one of the most prominent and influential musicologists in post-World War II America. 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. He did significant work preparing editions of Renaissance composers and was a major figure in redefining standards for critical editions of musical manuscripts. 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.