The company confirmed the news in an emailed statement.
A spokesman said the firm was in mourning over the “loss of the former Nintendo president Mr Hiroshi Yamauchi, who sadly passed away this morning.”
He died of pneumonia at a hospital in central Japan, the company said, adding that a funeral will take place on Sunday.
Mr Yamauchi ran the company from 1949 until 2002.
In that time, he took what was a small-time collectable trading card company and built it into one of the most recognisable – and successful – video games brands today.
“Hiroshi Yamauchi transformed a run-of the-mill trading card company into an entertainment empire in video games,” said Ian Livingstone, co-founder of Games Workshop and former chairman of publisher Eidos.
“He understood the social value of play, and economic potential of electronic gaming. Most importantly he steered Nintendo on its own course and was unconcerned by the actions of his competitors. He was a true visionary.”
Rob Crossley, associate editor of Computer and Video Games magazine, told the BBC: “You cannot overestimate the influence the man had on the games industry.”
“He spearheaded Nintendo as they moved into the arcade business, with hits such as Donkey Kong.
“This man was the president of Nintendo during the NES, the SNES, the N64 and the Gamecube – the first two were transformative pieces of electronic entertainment.”
Mr Yamauchi took over at Nintendo after his grandfather suffered a stroke. After several years developing the firm’s existing trading card business, Mr Yamauchi turned to electronic entertainment.
He utilised the work of legendary games designer Shigeru Miyamoto, who had made Donkey Kong, as a way of breaking into the US arcade game market.
Mr Miyamoto’s later work was pivotal in the success of Nintendo’s home entertainment systems – titles such as Super Mario, Legend of Zelda and Starfox became commercial smashes and household names.
Mr Yamauchi stood down as president in 2002, taking a place on the firm’s board of directors. In 2005, he left the company entirely.
Since his departure, Nintendo has gone on to produce the hugely successful Wii console, but has floundered in the past 12 months due to disappointing sales of its latest effort, the Wii U.
Mr Yamauchi, one of Japan’s richest men, also used to own the Seattle Mariners major league baseball club before selling it in 2004 to Nintendo’s US-based operation.