Freshman quarterback John O'Korn threw for 281 yards and three touchdowns, and Houston overcame a sloppy start to survive Rice 31-26 on Saturday afternoon.
Alex Lyons returned a blocked field goal 61 yards for a touchdown with 2:19 to go in the game to get Rice close, but the Owls missed on the two-point conversion.
Rice recovered the ensuing onside kick at its 47-yard line but was unable to score.
Deontay Greenberry and Ryan Jackson each caught a touchdown in the second half to help lead the Cougars (3-0).
Greenberry finished with 146 yards receiving on six catches, including a 61-yarder from Korn in the first quarter to set up Houston's first score.
Jackson also rushed for 87 and a touchdown on 19 carries.
Senior Taylor McHargue went 21-for-36 for 232 yards, and Turner Peterson finished with 102 yards and a touchdown on five catches for the Owls (1-2).