After I got the portal stone, I got the quest to go to the Neopolis. I tried to go in, but it wouldn't let me.
Does your quest say "Explore the Necropolis" ? If so, click on the dialogue bubble (the question mark in the upper left corner of the quest box), and read what you are supposed to do, and follow your yellow quest helper arrow.
For the first time in the Necropolis, you can't go thru the portal. After your first visit, then the portal works for you.