The Royal Swedish Academy of Sciences said the two researchers had made key contributions to experiments showing that neutrinos change identities as they whizz through the universe at nearly the speed of light.
Neutrinos are minuscule particles created in nuclear reactions, such as in the sun and the stars, or in nuclear power plants.
There are three kinds of neutrinos, and the laureates showed they oscillate from one kind to another, dispelling the long-held notion that they were massless.
“The discovery has changed our understanding of the innermost workings of matter and can prove crucial to our view of the universe,” the academy said.
Kajita, 56, is director of the Institute for Cosmic Ray Research and professor at the University of Tokyo. McDonald, 72, is a professor emeritus at Queen’s University in Kingston, Canada.
The winners will split the 8m Swedish kronor prize money. Each winner also gets a diploma and a gold medal at the prize ceremony on December 10.
Kajita and McDonald made their discoveries at the Super-Kamiokande detector in Japan and Sudbury Neutrino Observatory in Canada, respectively.
Kajita showed in 1998 that neutrinos captured at the detector underwent a metamorphosis in the atmosphere, the academy said.
Three years later McDonald found that neutrinos coming from the sun also switched identities.
McDonald told a news conference in Stockholm by telephone that the eureka moment was when it became clear that his experiment had proven with great accuracy that neutrinos changed from one type to another in travelling from the sun to Earth.
The prize announcements continue with literature today, the Nobel Peace Prize on Friday, and the economics award on Monday.