First of, if you have a firewall like CSF you will need to allow the new port though the firewall.

Then type the following command: nano /var/cpanel/cpanel.config

change the port by: port=2082 to port=6060 (whatever your new port will be)

Please do not use the port above incase a bot has checked this Article.

After you've changed the port run the following commands:

/usr/local/cpanel/whostmgr/bin/whostmgr2 --updatetweaksettings

/etc/init.d/httpd restart

That will allow that new port to take effect.