First some background. At the end of 2012 we migrated our vs2008 solution to vs2010 but we still target .NET 3.5. (I know nothing but the latest and greatest here!)
As I was searching how to solve this one, almost everyone recommended either to copy the missing MSBUILD folder or install some SDK of some version.
Luckily, I've found this awesomely helpful post by Donovan Brown : http://donovanbrown.com/post/So-sick-of-MicrosoftWebApplicationtargets-was-not-found-build-errors!
In a nutshell, the idea is to configure the VisualStudio version your build should use in your Build Definition:
Right Click -> "Edit Build Definition..."
Go to "Procss" -> "3. Advanced"
and set "MSBuild Arguments" with
/p:VisualStudioVersion=12.0