San Jose (7-12-9) trails the last playoff spot by five points with two games left.
Holden scored in the 93rd minute on a rebound of Nate Jaqua's shot after he hit the left post with a shot from the left box. With San Jose goalkeeper Joe Cannon drawn to the left, Holden came through the middle of the box and one-timed it into an open net.
Holden's goal helped Houston win despite being a man down for most of the match after forward Kei Kamara was red-carded in the 11th minute for an elbow to San Jose's Nick Garcia.
Houston defender Eddie Robinson kicked a back pass to goalkeeper Pat Onstad in the 68th minute, but Robinson kicked it short, and Onstad had to make a sliding kick to try to clear it. The goalie's clearance, however, went right to Scott Sealy, who tied the game with a line drive from 25 yards out on the right side into the empty net.
Holden gave Houston the lead in the sixth minute with a rebound of Kamara's header.