I just created a webform that is hosted in my Azure subscription. I set it up with authenication via my works Azure directory for authenticating users. In debug this works f
I have solved this issue. Since it was such a pain I will keep this up as I couldn't find any answers on this. It was actually quite simple.
You have two options. The one I did and which worked was changing the publish profile as below:
Add the domain where the authentication is occurring. So if you have your web app hosted by a different azure account that which is authenticating the users, use the one that is authenticating.
This will create two versions of your app on the site one for local host and one for the actual site.
The second option(I have not tried this but it should work) is to go to the Azure account where you are authenticating the users and go to applications and then configure. Change the APP URL from local host to the url you are trying to get to.
Here is an excellent link that explains how to do this clearly.
Click this link for detailed explanation