Nonaka died on January 20, 2019, aged 113.
He was certified as the oldest living man in the world last year at the age of 112 years and 259 days.
Nonaka was born on July 25, 1905, 42 days before the Russo-Japanese War ended with the Treaty of Portsmouth, mediated by Theodore Roosevelt.
His granddaughter Yuko said Nonaka didn't have any health issues - he just passed away peacefully.
Mr Nonaka was one of around 68,000 people in Japan aged 100 or older.
"We feel shocked at the loss of this big figure".
He had six brothers and one sister, marrying in 1931 and fathering five children-two sons and three daughters. He was said to have enjoyed reading, watching television, eating candies after every meal, and soaking in a hot spring once a week.
Nonaka lived at home in Ashoro with his family.
His family said he spent his time enjoying hot springs at their inn, watching sumo wrestling on television and eating candies.
The oldest verified person - the French woman Jeanne Louise Calment - died in 1997 at the age of 122, according to Guinness World Records. Kane Tanaka is a 116-year-old woman who lives on Japan's southern main island of Kyushu, according to the AP.