Their existence was tentatively proposed in 1930, but was only proved in the 1950s, when nuclear reactors began to produce streams of the particles.
Kajita and McDonald will share the prize sum of eight million Swedish kronor (around $950,000 or 855,000 euros).
McDonald, formerly an Australian, 72, told the Nobel Foundation that winning the prize was “a very daunting experience, needless to say,” recalling the “eureka moment” when he made his discovery.
“Fortunately I have many colleagues as well who share this prize with me,” he added.
McDonald is a professor emeritus at Queen’s University in Canada.
Kajita, 56, meanwhile said “it was a real surprise to me. It’s kind of unbelievable.”
Asked whether he ever dreamed of winning the Nobel, he replied: “As really a dream maybe yes, but not a serious dream so far.”
He is the director of the Institute for Cosmic Ray Research and a professor at the University of Tokyo.
This year’s physics prize follows the 2002 award to Raymond Davis of the US and Masatoshi Koshiba of Japan, pioneers in the field of cosmic neutrinos.
Nobel week continues on Wednesday with the announcement of the winners of the Nobel Chemistry Prize.
The winner of the literature prize will be revealed on Thursday, while the peace prize will be announced in Oslo on Friday.
The economics prize wraps up this year’s Nobel season on Monday, October 12.
The laureates will receive their prizes in Stockholm on December 10, the anniversary of the 1896 death of prize creator Alfred Nobel, a Swedish philanthropist and scientist.