Using certificates in an Azure WebSite works differently to how it does in a local copy of IIS or even when running a web site in debug mode from Visual Studio. In short, the website does not have access to a certificate store in the traditional sense of the term ... it is all done in memory.
Firstly, once you have uploaded your certificate through the Azure portal you need to add an appsetting (also through the portal) called WEBSITE_LOAD_CERTIFICATES and set the value for this to the thumbprint of your uploaded certificate. This can be a comma separated list of multiple thumbprints if you want, or even * to load all your uploaded certificates. I'm presuming this forces the certificates to be loaded in to memory.
To then load your certificate, you can do the following:
var store = new X509Store(StoreName.My, StoreLocation.CurrentUser);
store.Open(OpenFlags.ReadOnly);
var certs = store.Certificates.Find(X509FindType.FindByThumbprint, YOUR_THUMBPRINT, false);
Change the 'false' to 'true' if you want to ensure the certificate is valid.
I found this information here, which explains it much better than I have: http://azure.microsoft.com/blog/2014/10/27/using-certificates-in-azure-websites-applications/
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…