If you refer to the actual text of the Tripartite Pact there's nothing there about killing the Jews, nor anything that would obligate Japan to follow Germany's orders with regards to its domestic population. In fact, it does quite the opposite and recognises a Japanese new order in East Asia, with a German-Italian new order in Europe. So, there would not have been any real point of tension with Japan refusing to follow German orders to kill the Jews, and--as far as I am aware--there never was any such directive sent from Berlin to Tokyo.

I've written more about the reasoning behind the German-Japanese alliance here.