From the command line this not supported. You will have to edit the packages.config file manually, or write a utility to do this work for you, or extend NuGet.exe with this feature.
There is no equivalent in NuGet to NPM's npm install -save
Currently the only way to have the packages.config file automatically updated when you want to install a new NuGet package to your project is to use an IDE, such as Visual Studio or Xamarin Studio, and actually install the package. Using NuGet.exe from the command line does not have an option to add/remove entries in to/from the packages.config file when installing a new package.
NuGet.exe does have an update command which will update the package to the latest version. Whilst this would update your packages.config file it also updates your project file by adding any assembly references that the NuGet package needs.