Is it possible to set the version number of the MSI when building a setup project(vdproj) from command line?

I need to build a setup project from command line and set the version number of the built msi from a parameter. Is it possible to accomplish that?

No, not possible. You'd have to rewrite the .VDPROJ as a prebuild step or update the MSI as a postbuild step. One of the many limitations of the toolset