First of all, please note that it is by no means accurate to say that the Japanese government has deferred to the emperor throughout history. There has actually been only a very short time in the modern era when the emperor had very much power. Outside of that, the emperor has generally been a figurehead.
The Japanese emperor holds his position because he is reputedly descended from the spirits through the first emperor, Jimmu. Jimmu was supposedly a descendant of both the sun goddess and the sea god. This made him and, therefore, his descendants, divine. However, this divinity has not typically given the emperor that much power. For much of Japanese history, Japan was ruled by shoguns with the emperor as a mere figurehead. This sort of rule lasted from 1197 AD to 1867. Around 1900, the emperor once again became a figurehead and power was truly held by the government which was dominated by the military. Today, the emperor has no real power.
The emperor has status because he is allegedly descended from the gods. But this has not meant that he has really had power for much of Japanese history.