Novotny studied art history at the University of Vienna under Josef Strzygowski, and wrote his dissertation on the Romanesque architectural sculpture in the apse of the Pfarrkirche ("parish church") in Schöngrabern, in Lower Austria.
As a result of this book, Novotny made the acquaintance of the painter Gerhart Frankl, whose own work was stylistically influenced by Cézanne, but had also struggled with his French forebear through his statements on the theory of art.
Despite his uncompromising anti-fascist attitude, in 1939 Novotny received a position at the Österreichische Galerie in Schloss Belvedere, where he served as interim director for two years immediately after the end of the war.
From 1960 until 1968 he served again as director of the Galerie, where he mounted a series of well-attended exhibitions that introduced the population of Vienna to the great masters of modern painting.
Novotny's study of Cézanne has been described as "the most disciplined exercise in the formal-analytic method" that was associated with the Vienna School of Art History in the mid-20th century.