I have two Azure Ad Apps:
1) Admin/BackendApp which guards my webapi
2) Consumer APP which will consume my webapi
When i try to access my web api using the token created using below URL passing the required ClientID, ClientSecret, Resource and grant_type=client_credentials
https://login.microsoftonline.com/XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX/oauth2/token
i get access token from above url and pass that token as Authorization header to my webapi i get successfull response without granting any access to/from admin/backendapp.