The Japanese aligned themselves with Germany and Italy for strategic reasons, not anti-semitism. I've never seen anything that indicates some sort of widespread anti-semitism in Imperial Japan. As mentioned in a previous /r/askhistorians answer, Japan's foreign minister stated:

I am the man responsible for the alliance with Hitler, but nowhere have I promised that we would carry out his anti-Semitic policies in Japan. This is not simply my personal opinion, it is the opinion of Japan, and I have no compunction about announcing it to the world.

The Japanese diplomat Sugihara Chiune is well-known for saving thousands of Jews from Europe, and whilst the conditions for Jews in the Shanghai Ghetto under Japanese control was far from ideal, its residents weren't targeted specifically for being Jewish.

One should point out that Japan aligned itself with Germany before Germany killed six million Jews. The anti-semitic policies of the Nazis predated the Final Solution, obviously, but the bulk of actual deaths in the Holocaust didn't occur until after the war was well under way.

The Japanese entered into alliance with Germany and Italy for strategic reasons, not anti-semitic ones. The Japanese might not have been anti-semites, and they clearly "knew" about Jews, but the Japanese government was clearly very willing to overlook Germany's anti-semitism to gain an ally. The alliance was initially formed in opposition to communism and the Soviet Union. That fell apart briefly when Germany signed a non-aggression pact and [entered into economic relations](https://en.wikipedia.org/wiki/German–Soviet_Commercial_Agreement_(disambiguation%29) with the Soviet Union, but in September 1940, Japan signed on to the Tripartite Pact. The Japanese thought that the Pact might keep the US out of declaring war on them if they committed to a "southern" expansion (attacking British and Dutch colonies), and it also allowed them to negotiate with Vichy France to station forces in Indochina.

The alliance between Germany and Japan was based more on interests and common enemies than it was on any sort of ideological connection.

source: A Modern History of Japan by Andrew Gordon