1) Web container is responsable to generate dinamic pages and executing specification of all objects created for this purpose -
servlet, filters,
JSP,
JSF etc...
2) Application Server or EJB Container is responsable to manage bussines layer and responsible for implementing the business layer of an enterprise application and specification of all the objects for this purpose - Stateless, Statefull, Message, Interceptors, Timer Services, Web Services etc...
Your confusion maybe cause the two can be running within the same product and host or separated into different product on many host... all depending on the application needs.
Regards.