With custom code, you could create an event receiver on the list where CSV file lives that will run some code whenever the CSV file is updated. Here's a starter:
http://elczara.wordpress.com/2011/02/16/sharepoint-2010-event-receiver/
Make it a farm solution (sandbox solutions can't write to the filesystem directly), and you'll probably want to look up RunWithElevatedPrivileges, since the user doing the uploading may not have permission to write to the file system.
Steve's suggestion of rethinking the end-to-end solution is a good one, although I'm not sure how you can trigger the other system to "do its business".