The Raptors had won five in a row after opening the season with a 4-19 record. Their winning streak came to an end in the opener of a three-game road trip.
Alan Anderson and Amir Johnson both scored 12 points for Toronto.
Toronto had been trying for its first six-game win streak in four seasons. San Antonio has won seven consecutive home games and the Spurs are 11-2 on their own floor this season.