It was the second straight win for the Magic, who have two exhibition games remaining. The Spurs lost consecutive games for the first time this preseason and host Washington Friday in their final regular-season tune-up.
Danny Green led San Antonio with 13 points and Manu Ginobili finished with 12 points. Tim Duncan played just 12 minutes, scoring nine points.
After playing sparingly in the Spurs' first four preseason games, Ginobili and Tony Parker played extended minutes for the second straight game.
Magic guard Arron Afflalo sat out again Sunday resting a sore left hamstring, but could make his preseason debut Wednesday against Memphis.