Nambu discovered the mechanism of spontaneous broken symmetry in sub-atomic particles, which granted him this recognition and half the US$1.4 million award.
Kobayashi and Maskawa share the other half of the prestigious prize for their work on predicting the existence of three or more families of sub-atomic "quark particles" in nature.
The committee said that, "The fact that our world does not behave perfectly symmetrically is due to deviations from symmetry at the microscopic level."
Kobayashi was shocked at the news exclaiming that, "It is my great honour and I can't believe this," as although the award is being given now their breakthroughs came in the 1960s and 1970s.
The Nobel Committee for Physics at the Royal Swedish Academy of Sciences awards this prize as the second of this year's Nobel awards.