A convent church was founded here around 1294 by the Augustinian hermits of Sant'Anna in Castello and named for Saints Augustine and Stephen.
Work on the current building began in 1294 and was finished in 1325, with major rebuilding in the early 16th Century. This latter work was overseen by Gabriele Veneto, an Augustinian worthy and scholar whose portrait was painted by Giovanni Bellini and who is very likely - a strong case has recently been made - the violist in Titian's mysterious and Giorgionesque The Interrupted Concert. Gabriele was buried in the new sacristy here and is commemorated on the lintel over its door. The church underwent further restoration in 1743.