Well, you can also ask yourself how could Naruto have talked to Minato in the Pein arc when Minato's Soul was sealed away. Minato sealed some of his and Kushina's chakra into Naruto which had their memories; so even though Minato's soul was gone, a part of it was still in Naruto. The Sage said his son's chakra transmigrated over time so a part of the son's chakra could have just been passed down is all.
