Miyazaki was nicknamed "Golden Bolt" in reference to eight-time Olympic gold medallist Usain Bolt after he clocked 42.22 seconds the day after his 105th birthday.
No previous world record existed when Miyazaki ran the time in his home city of Kyoto in 2015.
The Japanese centurion was born in 1910 and since then the 100m world record has been broken more than 15 times.
The real Bolt holds the current record at 9.58 seconds and the Jamaican star tweeted his admiration for Miyazaki after his achievement.
He said: "Shout out to 105-year-old Hidekichi Miyazaki of Japan who holds the record for the oldest sprinter to compete over 100m."
Miyazaki started running in his early 90s citing pre-race naps as the key to his success.
However, despite his impressive feat the elderly athlete was disappointed with his effort.
Speaking after the race he said: "I am not happy with the time.
"I started shedding tears during the race because I was going so slowly."
He then quipped: "Perhaps I'm getting old!"
The Japan Times reported that local officials confirmed he died on Wednesday.
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