Separating them is not going to stop the barking.
Is one barking more than the other?
He has learned that his barking will make you come out an interact with him. As long as you do it, the behavior will continue. There are a lot of sounds and smells that they encounter at night that can be stimulating (squirrels, possums, etc) so this could also be your problem.
They make correction collars for this sort of thing. One is a collar that is on a remote. It will blow a citronella spray in your dog's face when he barks. Then, of course, there are shock collars that you can use as well.
You might even want to consider bringing him indoors in a crate to sleep if he's a good dog.
Let me know if you still have questions.