if your program really reads from STDIN (update: instead of reading the terminal input directly - some unix programs read from /dev/tty for sensitive information, for example) and the command name really starts with a dash and you wouldn't try to redirect the output, it might work.

Try this:

my $pwd1 = "pwd1";
      my $pwd2 = "pwd2";
      open(FOO, "|$command") or die "open command failed: $!";
      print FOO "$pwd1\n$pwd2\n";
      close FOO;
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update 2: redirecting the output shouldn't have any serious consequences, but it may help in that it may show error messages that otherwise might get redirected