Private / introduction-only restaurants/bars/etc. aside, let's not pretend that there are not also many establishments in Japan that refuse service to foreigners, even if they are fluent in Japanese. It's rarer in central Tokyo, but in the Tokyo outskirts and even in central Osaka/Kyoto I've experienced it on many occasions.

OP - the extreme level of ingrained xenophobia is just something that you'll have to accept if you want to keep visiting Japan, unfortunately.