Houston (13-10-8) moved one point ahead of Montreal (13-10-7) for third place in the Eastern Conference.
Clark got the game's only goal after getting a shoulder pass from Giles Barnes in the centre of the field, settling the ball with his left foot and one-timing it with his right foot into the left net from 25 yards out.
Montreal's best chance to even things up in the first half came in the 41st minute off Marco Di Vaio's free kick from just outside the upper right box that was knocked out by a wall of Dynamo players. The ensuing corner kick was also cleared by Houston.
The Dynamo missed chances to extend the lead early in the second half as Clark sent a shot high in 48th minute before Brad Davis had a shot from the left box stopped on a kick save by Montreal goalkeeper Troy Perkins in the 51st.
Perkins kept the deficit one in the 53rd, batting Davis' free kick from outside the upper right box over the crossbar.
Will Bruin's header off Davis' corner kick in the 68th was stopped by Montreal defender Collen Warner and then cleared.
Montreal had a chance to tie it in the 70th after Houston goalkeeper Tally Hall came off his line, leaving the goal open, but Davy Arnaud's shot from 14 yards out in the middle was blocked by Houston defender Bobby Boswell.
The Impact remained on the offensive with second half substitute Andrew Wenger missing a short breakaway just wide of the near post from the middle box in the 72nd.