There is a possibility to achieve Multi factor authentication using Authenticator app. It is documented and a sample is provider here: Azure AD B2C: TOTP multi-factor authentication
With Azure Active Directory (Azure AD) B2C, you can integrate TOTP-based Multi-Factor Authentication
so that you can add a second layer of security to sign-up and sign-in experiences in your consumer-facing applications. This requires using custom policy
and custom REST API endpoint
. If you already created sign-up and sign-in policies, you can still enable Multi-Factor Authentication.
Below is the user auth flow using TOTP:

At this time, MS does not support primary Auth using Authenticator for B2C. You can request this via the Azure AD B2C forum in feedback.azure.com