First you need an alliance with the pope (works too without being allied with him only slower). All you need to do then is move multiple 1 unit armies into the territory of the enemy nation the pope favours too much. They will be attacked multiple times within one turn, you choose to withdraw as much as possible. Every time the enemy nation attacks your armies their relations with the pope will go down. Three turns should be enough to get any faction down to 1 cross favour if not excommunication. If you gave a border rpovince to the pope and the enemy armies chase you into papal territory his holyness will not be amused either.