Unable to revoke permissions for 'NT AUTHORITY\SYSTEM' on SQL Server 2016
This should revoke the permissions

REVOKE CONTROL SERVER TO [NT AUTHORITY\SYSTEM]
REVOKE SHUTDOWN TO [NT AUTHORITY\SYSTEM]




Tests

use [master]
GO
GRANT CONTROL SERVER TO [NT AUTHORITY\SYSTEM]
GO
use [master]
GO
GRANT SHUTDOWN TO [NT AUTHORITY\SYSTEM]
GO

EXECUTE AS LOGIN = 'NT AUTHORITY\SYSTEM'
SELECT * FROM fn_my_permissions(NULL,NULL)
REVERT


Result



... (34 Results)

REVOKE CONTROL SERVER TO [NT AUTHORITY\SYSTEM]
REVOKE SHUTDOWN TO [NT AUTHORITY\SYSTEM]

EXECUTE AS LOGIN = 'NT AUTHORITY\SYSTEM'
SELECT * FROM fn_my_permissions(NULL,NULL)
REVERT


Result





Extra info 

If you are ever unsure about the syntax, an easy one (in my opinion), is selecting what you need inside of the GUI and then scripting it out using the 'script' button. 

For example in this answer, I added the grants for the CONTROL SERVER and SHUTDOWN to the login NT AUTHORITY\SYSTEM , Scripted it out, and then removed them in the GUI and scripted them out again to get the revoke statements.
I am against executing stuff through the GUI though, since it is easy to overlook things, and it has proven to be buggy.