The Whitecaps could have two ahead at the interval when Darren Mattocks played in Morales and his effort needed a good save from Tally Hall.
However, they were awarded a penalty on 58 minutes when Kofi Sarkodie was adjudged to have handled the ball. It was left to ex-Scotland striker Kenny Miller to tuck away the spot kick.
Despite Vancouver largely controlling the game, they were pegged back with 15 minutes to go when Brad Davis crossed for Ricardo Clark, who swept the ball beyond David Ousted to set up a grandstand finish to the game.
Houston were almost level with five minutes remaining when David Horst found Giles Barnes, but the ex-Derby County man dragged his shot wide and the Texan side were unable to pull back the deficit.