How to tell git which private key to use?

From Git version 2.3.0, you can use the environment variable GIT_SSH_COMMAND like this:

GIT_SSH_COMMAND="ssh -i ~/.ssh/id_rsa_example" git clone example

Note that -i can sometimes be overridden by your config file, in which case, you should give SSH an empty config file, like this:

GIT_SSH_COMMAND="ssh -i ~/.ssh/id_rsa_example -F /dev/null" git clone example

Configuration core.sshCommand:

From Git version 2.10.0, you can configure this per repo or globally, so you don’t have to set the environment variable any more!

git config core.sshCommand "ssh -i ~/.ssh/id_rsa_example -F /dev/null"
git pull
git push