Well then I guess you'll have to implement a router in PHP yourself.
The tricky point will be that you need to direct any URL to a same PHP file where you can then handle the URL rewriting/re-interpretation.
What you can do is set the php.ini variable auto_prepend_file (http://www.php.net/manual/en/ini.core.php#ini.auto-prepend-file) so any request for a PHP file will first execute the prepended file. That's where you can then parse $_SERVER['REQUEST_URI'] and reroute the requests to the Phalcon app controllers accordingly.
But I'm a bit short on the Phalcon inside workings to explain you how you can then pass your request variables on to the framework engine... maybe someone else can help you with that.