Visual Studio has a special type of project, called Makefile Project, that allows you to use your own make file and other command line tools to build your project. See
MSDN VisualStudio 2005 Makefile Project
In such a project you can use for example Microsofts version of the make utility, called NMAKE, to build your project.
All this applies to VS 2005. I am not sure whether newer versions of VS still support this.