You need SSH key in order to enable SSH key pair login. You can read how to make in here How to create SSH key.
Once your SSH key is ready you need to copy it on your machine.
$ cat ~/.ssh/id_rsa.pub | ssh user@123.45.67.89 "cat >> ~/.ssh/authorized_keys"
Now you can check if everything went ok by:
$ ssh 123.45.67.89
Before you step ahead you need to check if you ssh key works fine. Now you can make root account accesible only by ssh key pair.
In order to achive this you need to log on the machine and do as follows (use your favourite text editor - vi, vim or any other):
$ sudo vi /etc/ssh/sshd_config
Now find the PermitRootLogin
section and change it like this
PermitRootLogin without-password
Exit editor and restart sshd service to put changes in action
$ reload ssh
Now in order to login on the machine as root valid SSH key will be necessary.
If something went south you can always use our web vnc client to connect to your machine.