After scoring two away goals at BBVA Compass Stadium, the defending champions will now be heavily favored to return to MLS Cup.
The away side opened the scoring off an 11th-minute corner as Gustav Svensson got in front of his marker to nod home, giving Joe Willis no chance.
Things went from bad to worse for Houston 15 minutes later when Jalil Anibaba pulled down Joeven Jones in the box, earning a straight red card for denying an obvious scoring opportunity.
But Joe Willis made a massive stop on the ensuing penalty, going down to his left to deny Nicolas Lodeiro.
However, Willis could do nothing just before halftime as Will Bruin victimized his old team with a picture-perfect header off a Jones cross to make it 2-0.
Houston had its chances in the second half but was unable to find the vital lifeline, and will now require a massive turnaround in the second leg.
The two sides will meet in the second leg at CenturyLink Field in Seattle on Nov. 30.