You've probably long since found a solution for this, but to elaborate on Tom Cabanski's answer, you can invoke Visual Studio to build the msi on the command line using "devenv.com" via an external process from within your build. It's not a pretty as using msbuild, but it gets the job done. Below is an example of how to invoke Visual Studio:
"C:\Program Files\Microsoft Visual Studio 9.0\Common7\IDE\devenv.com" your.sln /build Release
Where your.sln is the solution file for the solution you wish to build, and Release is the configuration you wish to build, ensuring that the configuration you choose actually builds the vdproj project.
Following the successful execution, you can grab the msi from the appropriate configuration's bin, and do what you want with it.
I'd appreciate your response to this with your findings/approach, as I'm trying to decide whether to adopt WiX or InstallShield as the approach to building msi's for Web Applications within TFS Build, or to continue with the approach I just described. I haven't had to opportunity to try WiX out, and my very limited exposure to InstallShield suggests that this is far to involved for my need, which is to produce a simple deployment aid for some relatively straight-forward web applications to the company intranet via TFS Build.