I have checked that in the web response the server is IIS when I deploy ASP.NET5 to azure web app, so I guess the IIS platform handler is used to redirect it to Kestrel. So
Your question is a bit ambiguous, as it asks at the same time about Azure Web Apps and about the general case. @Maxime answered the general part, so I'll answer the Azure Web App part.
It is not possible to bypass IIS in Azure Web Apps. Stack that normally run without IIS are typically handled using HttpPlatformHandler (as is the case for ASP.NET 5), or in the case of Node some variant of that (iisnode).