The Faction Border is charged with arcane power and prevents enemy factions from teleporting their cities into your faction's homeland. Be aware, however, that it doesn't stop their armies from crossing!
It also protects the Citadel and Fortresses in your homeland from being attacked by enemy factions. To push back an enemy faction's border, a faction must capture all adjacent Fortresses outside the border and hold them through the Contested Period (meaning the Region's color changes).