Gilbert was 23 of 38 for 265 yards with two interceptions for the Mustangs (3-4, 2-1 Conference USA), and Zach Line ran for 113 yards and two scores.
Darius Johnson led SMU in receiving with nine catches for 110 yards, Jeremy Johnson had nine receptions for 94 yards and a score, and Keenan Holman caught a 43-yard TD pass.
Taylor Reed, Darrian Wright and Stephon Sanders returned interceptions for touchdowns, and Kevin Pope scored on the fumble return.
Crawford Jones, David Piland and Bram Kohlhausen each threw two interceptions for Houston (3-4, 2-1). Jones also threw three touchdown passes.
Charles Sims had seven catches for 114 yards and two touchdowns, and ran for 54 yards and two more scores. D.J. Hayden scored on a 75-yard interception return.
SMU had 384 yards of total offense and Houston finished with 560.
Both schools are headed to the Big East next season.