It convinced the Japanese that the Nazis weren't really looking out for their interests. Prior to 1939, Japanese foreign policy had been aggressively anti-Soviet; a traditional rivalry with Russia over domination of Asia was married to an ideological hostility between the two. The Japanese justification for going into China was, in the final analysis, to root out communist influence -- they thought the Soviets were behind the GMD government (which had been true 10 years ago but wasn't by 1937). Similarly, the decision to move closer to Germany and Italy was motivated by desire to align Japan with anti-Russian, anti-Communist rising powers.

When the Molotov-Ribbentrop pact was announced, it floored the Japanese and actually collapsed the cabinet of the Prime Minister. They were quick to adjust, though; the Japanese signed on to a Neutrality Pact with the USSR the next year, and Foreign Minister Matsuoka Yosuke spoke at great length about creating an alliance of anti-Western revisionist powers comprised of the Soviets plus the Tokyo-Berlin-Rome Axis.

When the Germans went and reversed themselves again by invading Russia, it produced another scandal that eventually cost Matsuoka his job (not before he could do a huge amount of damage to US-Japan relations, though). From that point on, the Japanese basically stopped listening to the Germans, and instead switched to a policy of trying to grab what they could while relying on Germany to take the majority of the heat for them.

Sources: Eri Hotta, Japan 1941 is a good place to start. So is Waldo Heinrich's book (I forget the name), and Akira Iriye's Origins of WWII in Asia and the Pacific.

Can I ask a more specific follow-up question regarding Italy: is there any evidence that the breaking of the Molotov-Ribbentrop Pact had any bearing on the negotiations or implementation of the Italian armistice with the Allies in 1943?