Let me explain my situation, I have an azure website (with azurewebsites.net sub domain), and a custom domain.com, built with asp.net MVC

Both are being indexed by Google, but I've noticed the custom domain is being penalized and it doesn't show up in results, it only shows when I search for "site:domain.com" I want to remove and block the azurewebsites.net subdomain from Google. I've read the "possible" solutions:

• Adding robots.txt: won't work, because the subdomain and the domain are the exact same content, so subdomain.azures.net/robots.txt will lead to domain.com/robots.txt, removing the domain as well.
• Adding the tag, is the same situation as the previous point.
• I'm using a CNAME register to redirect the domain to the subdomain, so I can't redirect to a sub directory.

Do you have any other ideas?