if you still want to use approach based on user (aka service) account you have to force developers of the apps to use delegated permissions. If these apps are not under your control and they require app permissions (auth based on client id and secret) there is not that many options available:
- choose another app
- restrict access to the app like said here Grant tenant-wide admin consent to an application
When an application has been granted tenant-wide admin consent, all users will be able to sign in to the app unless it has been configured to require user assignment. To restrict which users can sign in to an application, require user assignment and then assign users or groups to the application