When i was playing earlier tonight i managed to get the AI down to its last City, but i could not take the city.  I just killed the enemy Sovereign over and over again but my troops would not be allowed into the city.  It appears that the enemy Sovereign was teleporting out of combat (like they should when they lose a battle) straight back to the city.

I just started playing the beta today, so I'm not sure if there is something else one needs to do to move an enemy Sovereign aside.