In the context of my limited knowledge of modern history, the two countries seem to have formed an unlikely alliance. So what am I missing? Was it strictly an economics issue?
Not an economics issue, but an ideological one.
In November 1936, Germany spearheaded the Anti-Comintern pact against the Third Communist International (in effect the Soviet Union). Signed by Japan (as well as others but we'll focus on Japan here) , it said neither nation would make treaties with the Soviet Union and both nations would support one another in case of attack by the Soviet Union. As well as being a grand anti-communist gesture by Hitler, it was hoped that England (who had been Japan's ally in World War 1) would also sign the pact and open the door to an Anglo-German alliance due to their dislike and distrust of Stalin. Suffice to say, this never came to pass. In 1937 Italy joined the pact, thus forming the last key major in the Axis powers.
Whilst Germany and Japan scarcely communicated at all during the war, they did honor the pact in some shape or form (though Germany did in effect break the pact by signing the Molotov-Rippentrop pact, a new Anti-Cominterm pact was drawn up in 1941), but mostly for their own reasons rather than the perceived greater Axis good. An example of this would be Hitler declaring war on America after Pearl Harbor (something Japan did not reciprocate against the Soviet Union it's worth noting)
(Sources: All Hell Let Loose by Max Hastings)