I keep important settings like the hostnames and ports of development and production servers in my version control system. But I know that it's bad practice to keep secrets (like private keys and database passwords) in a VCS repository.
But passwords--like any other setting--seem like they should be versioned. So what is the proper way to keep passwords version controlled?
I imagine it would involve keeping the secrets in their own "secrets settings" file and having that file encrypted and version controlled. But what technologies? And how to do this properly? Is there a better way entirely to go about it?

I ask the question generally, but in my specific instance I would like to store secret keys and passwords for a Django/Python site using git and github.
Also, an ideal solution would do something magical when I push/pull with git--e.g., if the encrypted passwords file changes a script is run which asks for a password and decrypts it into place.

EDIT: For clarity, I am asking about where to store production secrets.
This is what I do:

Keep all secrets as env vars in $HOME/.secrets (go-r perms) that $HOME/.bashrc sources (this way if you open .bashrc in front of someone, they won't see the secrets)
Configuration files are stored in VCS as templates, such as config.properties stored as config.properties.tmpl
The template files contain a placeholder for the secret, such as:
my.password=##MY_PASSWORD##
On application deployment, script is ran that transforms the template file into the target file, replacing placeholders with values of environment variables, such as changing ##MY_PASSWORD## to the value of $MY_PASSWORD.
How can I save my secret keys and password securely in my version control system?