Defender Joe Bennett was the unlikely goal-scoring source, making the breakthrough in the 41st minute as Villa beat the MLS club at BBVA Compass Stadium.
Paul Lambert's men have now won all three of their club friendlies, having accounted for Mansfield Town 3-1 and Dallas 2-0 in the United States on Wednesday.
Houston - second from bottom in the Eastern Conference - went into the match with one eye understandably on next week's must-win fixture with high-flying DC United.
Dynamo are in the midst of a nine-game winless streak in MLS and they were forced on the back foot for periods of the first half.
Villa had a good opportunity to open the scoring in the 38th minute when Andreas Weimann broke down the right wing but his cross was cleared for a corner.
Houston goalkeeper Tyler Deric was then forced into a save two minutes later after Fabian Delph tried his luck from outside the penalty area.
The deadlock was broken four minutes before the half-time interval as Bennett found himself unmarked in the box to head home Weimann's cross.
Lambert made wholesale changes at the break, introducing the likes of Darren Bent, Leandro Bacuna and Gary Gardner.
And while Villa worked themselves into a couple of threatening areas in and around the box, they did not add to their first-half goal as Houston pressed forward late in the game.
