Houston (6-7-6) won for the first time in four games, while San Jose (7-7-4) lost its second straight.
Ricardo Clark scored in the 10th minute after heading in Alexander Lopez's cross. In the 81st, San Jose misplayed a back-pass and Leonel Miranda ran on the loose ball, took three touches in open space and fed Bruin for an easy finish.
Houston's DaMarcus Beasley was stopped by goalkeeper David Bingham in the 56th minute. Clark one-touched the rebound but it was saved on the goal line by an outstretched Victor Bernardez.
Bernardez's free kick from just outside the penalty area hit off the post in the 32nd.
Several players were out because of international duty with the Gold Cup. San Jose was without Chris Wondolowski (USA) and Cordell Cato (Trinidad & Tobago). Houston was missing Boniek Garcia and Luis Garrido (Honduras) and Giles Barnes and Jermaine Taylor (Jamaica).