msbuild subfolder/myproject.vcxproj /t:build /p:Configuration="Release";Platform="x64";SolutionDir=MyPathToSln\
Make sure you don't use any absolute or relative path to the project, try to use path with $(SolutionDir)\MyPathToRessource and specify your path according to the provided SolutionDir from command line. This will save you a lot of problems in the long run. Also note the ending backslash for SolutionDir to help you with the difference between VS and MSBuild problem since VS always add it.
This will make it possible to use msbuild to build your project. Take great care with your references, since Visual Studio make many addin on the fly and things may work into Visual Studio and not into MSBuild. But modification for MSBuild are always a good thing for clean solution/project/dependencies anyway.
After that you can launch your msbuld command from Jenkins like any other cmd
also if you want to build (clean too) that project alone :
/p:BuildProjectReferences=false
If you need to make difference between the MSBuild and VS you can use the following variable into your conditions:
$(BuildingInsideVisualStudio)