The process by which you revoke the ability to run a privileged system procedure is dependant on the security model under which it runs.
For a privileged system procedure using the SYSTEM PROCEDURE DEFINER model, revoke the EXECUTE privilege on the system procedure from the user:
REVOKE EXECUTE ON sys_procedure_name FROM grantee [,...]
For a privileged system procedure using the SYSTEM PROCEDURE INVOKER model, revoke the underlying system privileges required by the system procedure from the user:
REVOKE system_privilege_name FROM grantee [,...]