You need to set the startupinfo parameter when calling Popen.
Here's an example from an Activestate.com Recipe:
import subprocess
def launchWithoutConsole(command, args):
"""Launches 'command' windowless and waits until finished"""
startupinfo = subprocess.STARTUPINFO()
startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
return subprocess.Popen([command] + args, startupinfo=startupinfo).wait()
if __name__ == "__main__":
# test with "pythonw.exe"
launchWithoutConsole("d:\\bin\\gzip.exe", ["-d", "myfile.gz"])