Rice scored in the third quarter when Sam McGuffie caught a 24-yard pass from Driphus Jackson. The two connected again for a touchdown on an 88-yard pass.
Houston (1-3, 1-0) opened its final season of Conference USA play before moving to the Big East.
Rice (1-4, 0-2) had hoped to rebound from an overtime loss to Marshall.
With the win, the University of Houston keeps the Bayou Bucket, the annual prize awarded to the winner of the Rice-UH game.