Since Certbot sets up Let's Encrypt certs by being installed a host machine, it wouldn't work with Azure Functions.
There are a few python clients available. You might be able to modify the code to work on Functions: https://letsencrypt.org/docs/client-options/#clients-python.
What might be the best choice is there is a 3rd party client already setup to work with Azure Functions: https://github.com/shibayan/appservice-acmebot. It is in C#, so if you don't want to deploy it as-is then it's not in one of your preferred languages. However, the similarities between C# and Java means that it still may be a good foundation for you to start with if you wanted to implement it yourself.