Yasutaro Koide, who was born on 13 March 1903, was officially named the oldest man by Guinness World Records in August last year.
At the time he was quoted as saying his secret to long life was not smoking or drinking, not to overdo things and to "live with joy".
Officials said he died of heart failure and pneumonia early on Tuesday.
It is not yet clear who succeeds him as the oldest man.
The title of world's oldest person is held by American woman Susannah Mushatt Jones, who is 116 years old.
She took the title last year after the death of Misao Okawa in Japan at the age of 117.
The oldest person who has ever lived according to Guinness was Jeanne Calment of France, who lived 122 years and 164 days. She died in August 1997.
The world's oldest man has died at the age of 112 in the Japanese city of Nagoya, local officials say.