I still think the northern most island of Japan, Hokkaido, could survive. It has a much lower population and gets cold in the winter. Especially since Japan was one of the first countries to close boarders along with Iceland, and magic has returned. Likely there would be kamikaze (in the literal meaning of divine wind) protecting them from infected from other lands try to get there.
I've said it before, but I'll say it again:
Just
imagine the scenario in which a storm sets in when the world infection is peaking, vanquishing or denying any would-be refugee fleets that may carry the rash. Basically a third Kamikaze. Then magic returns.
The Shinto faith would experience an explosive rebirth.
Japan would probably succumb to the rash eventually in any case. It's geographically a huge country, and most of it quite warm as well. You just need that one beached beast whale.
And with the almost inevitable collapse of its current central government due to famine, there wouldn't be anyone capable of mounting any sort of swift response.
Even with surviving civilization in Northern-Japan, those would be some extremely brutal first years, with or without the rash.