Two second-half goals from the Orange canceled out and eclipsed Darren Mattocks' sensational opener.
Vancouver scored the opening goal in the 36th minute. Darren Mattocks stumbled at the top of the box going past Eric Brunner, but recovered enough to blast home a fantastic curling strike from 20 yards out.
But Houston has earned a fearsome reputation when playing at home, and the Dynamo struck back with two goals in the second half. Giles Barnes got the equalizer in the 55th minute, leaping high to put his head into Ricardo Clark's fantastic cross as the Vancouver defense left the Englishman unmarked.
Warren Creavalle then put the Orange up in the 62nd minute. Will Bruin got a touch on Brad Davis' corner, and Creavalle was in position to poke it home for the lead.
The result means the first loss of the season for the Whitecaps, leaving fellow Canadian side Montreal as the only team left in MLS with a prefect record.