I just used my Discover Card at a few places in Japan:
Prince Park Tower hotel (I understand many hotels accept Discover Card now in Japan), restaurants and stores in Tokyo. I was even able to get Cash at the JCB ATM machine in the airport (by the departure gate).

Just keep trying it! My understanding is that even if it is not accepted right now, it will be by later this year. (That's the buzz I heard in Japan)!