We've been using Duo Security for two factor ssh auth[0] for a number of years. Its quite easy to setup and gives you push notifications to your phone. Its awesome.
(Hopefully you'll have configured things so that Duo's approval and a password are both required for login, so this isn't a catastrophic break in security, but it's still a little worrying. And what about when your Internet connection, or Duo's, is having problems? As I write this comment, HTTPS connections to www.duosecurity.com are throwing errors because they've installed a certificate for *.test.duosecurity.com. [1])
I prefer Google's pam_google_authenticator module. Like the Android/iOS app, it doesn't have any external service dependencies; all it assumes is reasonable clock synchrony.
[1]: https://www.ssllabs.com/ssltest/analyze.html?d=www.duosecuri...