Find out how to fix this here:

https://github.com/blog/1614-two-factor-authentication#how-does-it-work-for-command-line-git

How does it work for command-line Git?

If you are using SSH for Git authentication, rest easy: you don't need to do anything. If you are using HTTPS Git, instead of entering your password, enter a personal access token. These can be created by going to your personal access tokens page.