A pair of Englishman scored for Houston as they stunned their Premier League opposition at BBVA Compass Stadium, with midfielder Andrew Driver curling a free kick home in the 10th minute and Giles Barnes capping off the victory with an 88th-minute strike.
New Stoke manager Mark Hughes started former Dynamo defender Geoff Cameron as part of the visitors' back four, while former PSV Eindhoven left-back Erik Pieters was handed a debut for the Potters.
Houston hit the front in the 10th minute after Ricardo Clark was fouled 25 yards from goal and Driver stepped up, curling a free-kick over the wall and out of reach of Stoke goalkeeper Asmir Begovic.
In an impressive performance, Houston wrapped up victory with two minutes remaining when Corey Ashe picked out Barnes, who slotted the ball home from a tight angle.
Stoke will continue their pre-season trip to the USA with a friendly against FC Dallas on Saturday.