Clark made his debut Monday with the Astros losing 7-3 to St. Louis for their eighth straight defeat.
Cooper, 59, became the Astros' manager in August 2007 after being the bench coach. Houston had an 86-75 record in 2008 and Cooper's contract was supposed to keep him with the team through 2010.
However, Houston had gone just 70-79 this season before Monday and slipped into fourth place in the NL Central.
"Decisions like this are never easy, but we believe that a change in direction on the field is in order," said Houston General Manager Ed Wade. "By making the move today, we will have the ability to evaluate other facets of our operation as we move into the offseason."