One of the key parts of Confucianism is that the ruler and ruled has certain obligations in their relationship. This unfortunately was not quite the case in Japan, because of certain prior trends:

Gekokujo (下克上): Literally "Under rules upper," this concept was the idea that lower ranking people can ruler higher ranking ones through power. The Sengoku period broke the power of the shogunate for a time, and some vassals overthrew their liege lord. In addition, groups of peasants and monks broke free of the daimyos and established somewhat independent realms. These groups became known as the Ikko-Ikki. This sort of idea established a precedent that would haunt Japan in the days up to World War II.

Rangaku (蘭學): While foreigners were mostly banned after the Tokugawa Shogunate obtained power, the Dutch were allowed to continue to trade outside of Nagasaki. This meant Western ideas and philosophy continued to enter Japan at Kyushu, where the clans closer to this area were able to develop. This created a gradual shift in power, and the end result was that the regions more exposed to the West were more able to adapt to modern technology and ideas than more isolated areas.

Sekigahara: This is actually a battle, not a concept. But what happened was two of the great clans that opposed the Tokugawa, the Mori clan of Nagato province and the Shimazu clan of Satsuma, had a conflict. The Mori clan was essentially persuaded/bribed to turn against the Shimazu clan by the Tokugawa, and Shimazu was defeated. But after the battle, the Mori were stripped of some of their lands, thus earning significant antagonism against the shogunate. There was a story how every year, the Mori clan had a tradition, where retainers would ask the clan head "Is it time to overthrow the Shogunate?" upon which the clan head would reply "Not yet, the shogunate is too strong." Of course, the Shimazu were also upset with the Tokugawa, having been humiliated in defeat. The only thing that really stopped any revolt was that due to the above incident, Shimazu and Mori were as furious with each other as they were against the Shogun.

Western influences: This was what broke the camel's back. Japan was aware of China's fate of being carved up like a meat roast by the colonial powers. The only way to survive was to adapt not only Western technology but Western ways, from centralization and imperialism to clothing and (limited) democracy.