did you deploy all ASP.Net MVC files to bin folder together with other assemblies? In Azure there is no GAC so all dlls should be deployed to bin. E.g. for MVC5 these files are needed:
Microsoft.Web.Infrastructure.dll
System.Web.Helpers.dll
System.Web.Mvc.dll
System.Web.Razor.dll
System.Web.WebPages.dll
System.Web.WebPages.Deployment.dll
System.Web.WebPages.Razor.dll
Also check other steps in this article: Migrate your .NET web app or service to Azure App Service.