Aron Baynes scored 16 points, and Danny Green and Marco Belinelli each added 12 points in San Antonio's preseason finale. Tim Duncan had six points and eight rebounds in 23 minutes, while Tony Parker had eight points and four assists in 20 minutes.
Omri Casspi and Chandler Parsons each had 16 points and Jeremy Lin added 11. Houston closes its preseason schedule Friday at Memphis before opening the season at home Wednesday against Charlotte.
Howard and Harden played all but the final minute of the third quarter, and the Rockets outscored the Spurs 37-25 in the period.
Boris Diaw and Belinelli started for Kawhi Leonard and Green. Leonard and Manu Ginobili both sat out the game to rest for San Antonio's season opener at home Wednesday against Memphis.