The 62-year-old admits his decision to evade taxes by using a secret bank account in Switzerland amounted to the "biggest mistake" of his life and he confirmed he will not be appealing Thursday's judgement by the Munich state prosecutors.
That stance flies in the face of the initial claims of his defence solicitor Hanns Feigen, who announced an appeal would be made in the wake of Thursday's verdict.
"After discussions with my family, I have decided to accept the decision of the Munich state prosecutors regarding my tax issues," Hoeness wrote in a statement on Bayern's website.
"I have asked my solicitors not to appeal the decision. That reflects my views on decency, conduct and personal responsibility.
"Tax evasion was the biggest mistake of my life and I will face up to the consequences of this mistake.
"I will also be resigning from my position of president of Bayern Munich. By doing this, I would like to prevent any damage to my club.
"Bayern Munich are my lifetime's work and they will remain such. I will remain attached to this amazing club and its people in a different way for as long as I live.
"I would like to thank all my personal friends and the supporters of Bayern Munich from the bottom of my heart for their support."
After learning of an investigation by a German magazine into German tax evaders using accounts in Switzerland, Hoeness voluntarily approached the German tax authorities to admit his actions early last year.
However, a four-day trial in Munich this week revealed that Hoeness had evaded far more taxes than he had declared, with the initial amount of 3.5million euros rising sharply to over 28million euros.
Friday's announcement brings an end to Hoeness' long involvement with Bayern, having first joined the club as a player in 1970.
After ending his playing career due to injury in 1979 he moved into a managerial role, becoming the youngest general manager of a Bundesliga club in the history of German football.
He held that position for 30 years before being elected club president in 2009 after Franz Beckenbauer stepped down.
Bayern moved quickly to fill the vacancy left by Hoeness' departure with adidas chairman Herbert Hainer elected as his replacement.
Hainer, 59, will assume Hoeness' duties after the club accepted his earlier resignation.
Hainer received a majority vote in an emergency board meeting on Friday and assumes his new position with immediate effect.
"Uli Hoeness has always served Bayern Munich's best interests with his leadership qualities, his high personal involvement and his exceptional lifetime achievements," Hainer said in a statement.
"He has made a considerable contribution to Bayern Munich becoming one of the most successful and attractive clubs in the world, financially and sportingly, and we will always be extremely grateful to him for this."