Hoeness, 62, a household name in his country and friend of Chancellor Angela Merkel, had admitted evading taxes on income earned in secret Swiss bank accounts but hoped for leniency in one of the most scrutinised cases of its kind ever in Germany. (Agencies)
"After discussions with my family I have decided to accept the ruling of the Munich court on my tax affairs. This befits my understanding of decency, dignity and personal responsibility," he wrote in a statement published on the Bayern website.
"Tax evasion was the biggest mistake of my life."
Judge Rupert Heindl ruled on Thursday that Hoeness's voluntary disclosure was incomplete and therefore did not meet a vital requirement of amnesty laws designed to encourage tax dodgers to come clean.
Hoeness, a former star footballer adored by Bayern Munich fans, had been a popular TV talk show guest and ironically had spoken out for higher taxes and railed against tax evasion.
"The chancellor respects the decision Mr Hoeness took today," Merkel's spokesman Steffen Seibert said. He declined to give details of a lunch between the chancellor and Hoeness that took place the day before Hoeness decided to turn himself in - a meeting that has been the subject of media speculation.
The case hinged on the question of whether Hoeness, who as a player helped West Germany win the 1974 World Cup, cooperated fully with his voluntary disclosure. The court decided he took too long to provide information, and it was riddled with errors.
His case profoundly shocked Germany, where tax evasion is considered a serious crime, and prompted thousands of tax dodgers to turn themselves in.
It caused deeper shock than when Peter Graf, the late father of former tennis champion Steffi Graf, was exposed as a tax cheat during the height of her career. He was sentenced in 1997 to three years and nine months for evading 12.3 million marks (6.3 million euros) and released after 25 months.
Hoeness, 62, a household name in his country and friend of Chancellor Angela Merkel, had admitted evading taxes on income earned in secret Swiss bank accounts but hoped for leniency in one of the most scrutinised cases of its kind ever in Germany.