There is no built-in option to clear the Cloudfront cache (not via an API).
But if Amazon Cloudfront offers you a public url that triggers the clearing of cache, then you can query that url through Cache Cleaner (see the system plugin settings).
CDN for Joomla! Only controls the url of the files used in your website. It does not control if and how your CDN provider (Cloudfront) caches your files.
Again, something you would have to ask Amazon Cloudfront support about.