Whenever you need to delete a super administrator user account in Joomla!, if you do it in the classic way (select the super administrator and click "Delete") a message will be displayed in the backend panel saying: "You cannot delete a Super Administrator."

To be able to do that, first you need to change the Group that it belongs to from "Super administrator" to something else. You can choose from "Administrator", "Manager" to "Registered" user. Changing the group means changing the super administrator rights.

Now, the super administrator can be deleted by selecting the user, than clicking on the "Delete" icon.