SharePoint 2013 - All Users - "Sorry, this site hasn't been shared with you."

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Error Message:

All Users, including Site Collection Admins & Farm Admins, are getting "Sorry, this site hasn't been shared with you" while trying to access any site collection under a web application

Solution:

If you set the Super User & Reader Accounts to a domain account for the Web Application(s) using PowerShell, make sure they have been added to the Web Application(s) via Central Admin with the appropriate rights.

 

More Information:

By default, the Portal Super User account is the site’s System Account, and the Portal Super Reader account is NT Authority\Local Service.

https://technet.microsoft.com/en-us/library/ff758656.aspx