As per what I found here, I had to run the domainjoin-cli as such direclty after logging into the server via SSH with root:
/opt/likewise/bin/domainjoin-cli join <domain> <account>
example:
/opt/likewise/bin/domainjoin-cli join domain.company.com jdoe
Without the path I got command not found.
Trying to name my host with the FQDN did not help (it would take it on the web, but after reboot it wouldn't be there). I did add entries to the hosts file but that didn't enable me to join through the web interface. Not sure if modifying hosts was needed for the domainjoin-cli to work. I did notice that after the join it listed the domain on the website in all-caps. Not sure if that mattered or not, as I only ever did Domain.Company.com.
This was on a fresh install of VMware vCenter Server Appliance 5.1.0.5300 Build 947940.
After joining and rebooting, I still could not see the domain under the permissions section. Looks like I may have to follow this and maybe this.