With Certbot, you would use
fullchain.pem instead of cert.pem, that's all. fullchain.pem contains cert.pem and the Letsencrypt intermediate certificate, that's the missing certificate.
Isn't there a file chain.pem or fullchain.pem?
If chain.pem, combine cert.pem and chain.pem (via a normal txt editor) in one file and use that.
If not, download it from
the R3.