Palguta took a pass from Caleb Folan and drilled the eventual winner through traffic from the upper center box into the right side of the goal in the 84th minute.
Houston had its six-game unbeaten streak snapped, while Colorado won for the first time since a 4-1 victory over D.C. United on April 3.
The Dynamo took a 1-0 lead in the 71st minute when Colin Clark sent a left-footed shot inside the near post from 16 yards out.
Colorado tied it 3 minutes later when Jamie Smith took a free kick from 45 yards out on the left sideline and blooped it over Houston goalkeeper Tally Hall.
The Dynamo had a chance to tie in the 86th, but Alex Dixon's shot from the right box was saved by Matt Pickens.