Up 25-12 at one point in the first half, the Pirates went to the locker room at the break only up by one at 26-25.
ECU senior Kenyatta Brown gave ECU its final lead at 40-39 with 9:57 to play, but Houston went on a nine-point run and wrested control of the game away.
Although ECU held a 37-30 rebounding advantage in the game, the Pirates shot a woeful 29.6% from the field including only 25.9% from 3-point range. Conversely, the Cougars shot 46.9%.
George Williams had 12 points for Houston, with Patrick Okafor and Marcus Oliver each adding 11. Travis Holcomb-Faye led ECU with 12 points.