Bruin scored off Giles Barnes' cross in the 51st minute to give Houston (7-12-4) the lead. Goalkeeper Andre Blake — making his MLS debut — guarded the near post to guard against Barnes, leaving an open net for Bruin.
Philadelphia's best chance of the second half came when Fred slipped a ball inside to Andrew Wenger, but his shot was saved by goalkeeper Tally Hall. Houston's ensuing counter-attack forced Blake to make two diving saves against Bruin.
Omar Cummings' cross deflected off Philadelphia defender Raymon Gaddis and rolled into the net in the 90th minute.
Philadelphia (6-9-9) had its five game undefeated streak ended.