Will Bruin's late winner was enough to see Houston take all three points from San Jose in Robertson Stadium.
Khari Stephenson gave San Jose the lead in the 40th minute when Sam Cronin ignited the attack and put Steven Beitashour into space, allowing the right back time to cross for Stephenson, who volleyed it home.
The lead would last until just after the break when Brad Davis earned a penalty for Houston after being tripped by Bobby Burling. In the first half, Davis had been booked for a dive in the box, but the referee pointed to the spot this time. Davis put the penalty away to level the score and set up the dramatic finish.
Luiz Camargo set the table for Bruin after finding space down the right and putting in a cross that led to the forward's clinical finish and a big win for Houston.
"Last year we found a way to win these games," Chris Wondolowski said. "This year we are shooting ourselves in the foot a bit. We are making a couple of mistakes and getting punished for them and not finishing when we should."