The mysql root password is not used for user authentication in the ispconfig interface. ISPConfig connects to mysql with the user "ispconfig" and not root. The root user is only used to create new client databases. Have you changed the password of the ispconfig mysql user too?
I couldn't find a way to restart ISPConfig 3 after these changes, or if it's even possible.
ispconfig is no daemon, so it has not to be restarted.