The court in the city of Fukuoka found that Nomura Satoru, aged 74, had ordered four assaults, one of which resulted in death.
The verdict came despite a lack of direct evidence against Nomura, local media said. He denied any involvement.
It is believed to be the first time a senior member of Japan's mafia, the yakuza, has been sentenced to death.
"I asked for a fair decision... You will regret this for the rest of your life," Nomura told the presiding judge after his sentencing on Tuesday, according to Japan's Nishinippon Shimbun newspaper.