Web applications are implemented leveraging the same technologies normally used for web site development, that is (in our case) LEMP systems and the SilverStripe framework.
The differences between the two cases is often blurred: a web site is generally browsed passively (hence more HTML and CSS) while a web application should be much more interactive (hence more JavaScript and PHP). In real world you often meet mixed requirements, e.g. web sites that have a section that should be browsed (static site) and a section much more dynamic (back-office).