Here is a short description on how I use my Nitrokey Pro to do Git operations on my GitHub repositories. Prepare your SSH client as described here.
The first step is to deposit the SSH pubkey at your GitHub profile. Go to Settings -> SSH and GPG keys and click on New SSH key. Set the title to Nitrokey and fill the Key field with your SSH key that you can dump to console with the following command:
$ gpg --export-ssh-key <user-id>
With that being prepared, change the remote of your repository to SSH:
$ git remote set-url origin git@github.com:pavel-pi/my-repo.git
Now you will need to have your Nitrokey plugged in for every Git operation you’ll do on that project.