Alfred Werner was born Alfred Weintraub on March 30, 1911. Both his mother, Frederika (née Silberstein) and father, Ignatz Weintraub, were born in the former Polish city of Lwow (Lemberg), but relocated to Vienna in 1898, where Ignatz studied law at the University of Vienna, and where both Alfred and his brother Edward (1914) were born. Both sons followed their father into the study of law, although Alfred was encouraged early by his teachers to study philology.

Werner studied law at the University of Vienna from 1929 to 1934, but also took courses in German literature, philology, pedagogy, history, and geography, with aspirations of a teaching career. After his graduation from the University, he continued his literary pursuits, writing for the Jewish publication Die Stimme and Gerechtigkeit, and publishing a volume of poetry under the title Gebet aus der Tiefe in 1936. During this time, he also lectured at the extension division of the University of Vienna and acted as literary director of the Jüdische Kulturstelle in Vienna. His career was cut short when he was arrested in 1938 and sent to the concentration camp Dachau, where he spent nearly a year, until he was allowed to immigrate to England in 1939. During the summer of 1940, Werner was again briefly interned, this time in the Kitchener Camp near Sandwich, England, awaiting a U.S. visa. Werner wrote articles for the camp publication, The Kitchener Review, and continued to write poetry describing his experiences of exile and internment.

In 1940, Werner arrived in New York City, spent a year mastering his English language skills, and by 1941 was freelance writing articles and reviews for the The New York Times, Kenyon Review, Commentary and Arts Magazine. He became an editor for the Universal Jewish Encyclopedia in 1941 and continued until 1945. During the late 1940s, Werner continued to pursue his freelance career and also held editorial positions on the Chicago Jewish Forum and later Survey Reports.

Werner spent the years from 1949 to 1952 absorbed in the study of art history at the Institute of Fine Arts of New York University, the beginning of his career as an art historian and serious art critic. From 1953 until his death in 1979, Werner published no less than 20 monographs on such artists as Ernst Barlach, Marc Chagall, Edgar Degas, Amedeo Modigliani, Chaim Soutine, Moses Soyer, and Max Weber, as well as over 2,000 articles and reviews on artists and art topics, including his regular monthly article series, "Views and Visions", for the magazine Art Voices.

Werner was married three times, but had no children. His first wife, Gertrude "Trudy", a psychoanalyst, emigrated with Werner to the United States in 1940, but died shortly thereafter. Werner married his second wife, Judith, in 1953, who died in the late 1960s. He was married to his third wife, Lisa, from 1975 until his death on July 14, 1979.