The club’s chief was jailed for three years and six months in prison after admitting evading more than €28 million in taxes on cash stashed in Swiss bank accounts.
In a statement on the club's website on Friday he said he was stepping down as president with immediate effect.
“After talking with my family I have decided to accept the judgment of the Munich court regarding my tax affairs.”
"I have instructed my lawyers not to appeal. This corresponds to my understanding of decency, conduct and personal responsibility. Tax evasion was the mistake of my life," he said in a statement.
"In addition, I resign with immediate effect from the offices of president of FC Bayern Munich and chairman of the supervisory board of FC Bayern Munich. I want to avert harm from my club.
"Bayern Munich is my life’s work and it will remain so. I will stay connected to this great club and its people in other ways as long as I live.
"I thank my friends and the fans of Bayern Munich from the bottom of my heart for their support."
The club and its top sponsors and shareholders – including Audi, Adidas, VW, Allianz and Deutsche Telekom – had supported Hoeneß since the tax scandal broke a year ago and remained silent after the verdict.
Few expected the 62-year-old, who helped make the club the most successful in the history of German football, to stay on as president.
“It’s still hard to imagine Hoeneß watching Bayern games on the TV in the common room of a prison rather than from the VIP area,” Bild newspaper wrote on Friday.
Despite his status as a legend of German football, there is little sympathy for Hoeneß and his predicament in the German press.
Hoeneß admitted in court to gambling on the stock market where he won millions which was then kept in the Swiss accounts.
“He brought it on himself,” Bild added.
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