Is it possible to encrypt all traffic between the last relay and my hidden service site? (I have tried to use an ssl certificate and configure tor like that:
HiddenServicePort 443 127.0.0.1:443 but it don't work)
If you're running a hidden service all connections from a Tor client to it are encrypted end-to-end
As already stated you may offer your service as a hidden service in addition to the public one. That way connections using the onion address will always be encrypted.
The Tor website has a manual for configuring a hidden service.