The ; character separates commands in most shells. What you've done is open a pipe from a shell which first runs env, then runs your custom_auth_tool with only password set. You need to either quote or backwhack the semicolon, or set the relevant keys in %ENV before opening your pipe. 

local $ENV{ QUERY_STRING } = "username=$uname;password=$pwd";
open( WEBOS, "/usr/bin/custom_auth_tool |" )
   or die "Can't open pipe to authtool: $!\n";
## ...

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In reply to Re: blank string returned from piped command by Fletch
in thread blank string returned from piped command by EvanK

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