You need to do:
require 'vendor/autoload.php';
use <NAMESPACE>\<LIBRARY>;
to load whatever your composer libraries are. composer.phar is the script that actually goes and retrieves libraries for you, based on the contents of your composer.json file.
If you want to actually run composer.phar from a PHP script, keep it simple and just use the shell (e.g. using backticks, shell_exec(), etc).
$output = `<path_to_composer>/composer.phar [options]`;
What you're trying to do is meant for libraries that have been packaged as a phar, not applications.