Think of a website as a place where a company provides information to their customers and prospect. They may collect an interest form or other simple information but the goal of a website is to provide information.
On the other hand, a web application is software that resides on the web. It could be a complex database, tools for processing data, a custom PDF reader, machine learning, or anything else. Though these tools reside on the Internet like a website they do more than what we generally think of a website doing.