Nakajima, who went on to appear as the iconic creature a dozen times, died of pneumonia on Monday, said a spokesman for the studio that produced the Godzilla films.
Originally a stuntman, Nakajima at the age of 25 first took on the role of the giant monster awakened by a hydrogen bomb test to rise out of a roiling sea and swim to Japan where it crushes Tokyo.
Godzilla, a walking, radiation-breathing analogy for nuclear disaster resonated in Japan. Just nine years earlier the country had suffered the world's first, and still only, atomic bomb attacks at the hands of the United States in the closing days of World War II.
The US also carried out a hydrogen bomb test at Bikini Atoll in the South Pacific in 1954, exposing a Japanese fishing boat to nuclear fallout, sickening the 23 crew and eventually killing the captain.
Nakajima prepared to play the imaginary creature by visiting a Tokyo zoo for a week to analyse the moves of elephants, bears and gorillas, according to the Toho website.
He said that the suit for the original film was too heavy and he could barely walk for 10 metres (33 feet). The suit weighed around 100 kilogrammes (220 pounds), Toho said.
Nakajima also said he "felt a sense of isolation" in the beginning because of the thickness of the rubber used in the suit that he could not remove without help.
"But I started to enjoy playing Godzilla," he said.
The franchise has produced 29 films in Japan, according to Toho.
The original movie "Gojira" -- a Japanese portmanteau of "gorilla" and "kujira" (whale) -- was a mega hit, drawing 9.6 million viewers to cinemas.