JRebel features Remoting facility, which can be used to sync the changes via HTTP to the remote machine. For that, you should enable JRebel on remote Tomcat (via -javaagent:jrebel.jar) and enable JRebel remote plugin that create an HTTP endpoint for negotiating with the IDE plugin. -Drebel.remoting_plugin=true will do.
For more information you can check the tutorial for setting up Remoting with IntelliJ IDEA and Tomcat.
Otherwise, without remoting enabled, you can deploy the app with the rebel.xml config file which will point to the location where the exploded application is and JRebel will make Tomcat to load the resources from that specific location, so you could just synchronize from IntelliJ to that remote location via SSH. JRebel will then work as usual - monitoring the changes in the specified location and reloading the classes/resources as soon as they are being used in the application.