I don't think Naruto's chakra is coming out of thin air. If you notice everyone in the shinobi alliance still had the one-tail shroud on them. This means that Kurama still had plenty of chakra left.
But darn, Naruto's feeling infecting everyone in the Alliance. Now they have a little grasp of his pain. Lovely chapter, now all I want to see is Kakashi, the Kages returning to the battle field and action.