Sonoda said at a press conference on Thursday it would be "difficult" for him to continue with his job in light of the accusations.
Japan's judo confederation confirmed Wednesday that Sonoda used violence after it was revealed that 15 female judoka sent a letter to the Japanese Olympic Committee at the end of 2012 complaining they had been subjected to harassment and physical violence by Sonoda in preparations for the Olympics.
"I deeply regret that my behaviour, words and actions have caused trouble," said Sonoda, a former world gold medallist in the men's 60-kilogram category. "It will be difficult for me to go any further with the training of the team."
Sonoda's resignation is the latest in a series of embarrassing incidents for Japanese judo. Last year, two-time Olympic judo champion Masato Uchishiba was accused of raping a teenager.
Japan failed to win a gold medal in men's judo at the London Olympics. The only gold for the nation that invented the sport was won by Kaori Matsumoto in the women's 57-kilogram division.
The use of corporal punishment in Japanese sports has come under the spotlight following the suicide in December of a Japanese high school student who endured repeated beatings by his basketball coach.