The 62-year-old resigned as both Bayern president and chairman of the club's supervisory board and was a noticeable absentee for 2-1 win over Bayer Leverkusen.
He stepped down less than 24 hours after being sentenced to three and a half years in jail by Munich regional court having cheated the state out of €28.5 million ($39.5 million) in unpaid taxes.
He admitted to hiding his wealth in secret Swiss bank accounts while obsessively "gambling" on stock and currency markets for years.
But while Hoeneß waits to start his time behind bars, the Bavarian giants already hope he will be back at the Allianz Arena soon.
"This club is one of the best in the world and that is down to the personality of Uli Hoeneß," said coach Pep Guardiola.
"He deserves our respect. I hope he can come back in the future and help us."
, Bayern named Karl Hopfner as Hoeneß' successor as club president.
Adidas' CEO Herbert Hainer, the CEO of German sportswear giants Adidas, takes over from Hoeneß as chairman of Bayern's advisory board.
Both positions must be ratified by a vote on at the club's general assembly.
But Edmund Stoiber, head of Bayern's management board, implied there will be a role for Hoeneß with the European champions following his release.
"A door is always open and Uli Hoeneß will always be the soul of the club," Stoiber told Die Welt.
"Whatever he wants to do, anything is possible."
Hoeneß's fall from grace comes with the club he built on the ascendancy and confirmed as the world's best domestic side after winning the Club World Cup last December.
There has been zero condemnation from within the tight-knit Bayern camp, even after the guilty verdict.
Chants of "Hoeneß - you're the best man!" could be heard at Munich's Allianz Arena during the win over Leverkusen.
Sky television underscored his absence when zooming in on the empty seat next to chairman Karl-Heinz Rummenigge where Hoeness normally sits and there were a few banners of support from fans.
"His resignation deserves the respect from FC Bayern and from all football fans," said Rummenigge.
"I am not a fan of the saying, 'the king is dead, long live the king', more of Franz Beckenbauer's sentiment that 'you never separate from good friends'.
"It's very hard to replace someone like Uli Hoeneß at the top of the club."
The club's stance has always been that the tax matters were personal choices made by Hoeneß, unconnected to his work as an employee.
His conviction tarnishes the image of his beloved Bayern, even if the club's success is directly entwined with Hoeneß' drive.
All five of Bayern's European titles in 1974, 1975, 1976, 2001 and 2013 came with him involved as either a player, general manager or club president.
Before his arrival as an 18-year-old in 1970, they had won just two of their 23 German league titles with a 24th imminent.
Bayern became Germany's first side to win the treble of Champions League, Bundesliga and German Cup under Jupp Heynckes last season, breaking or equalling 25 league records.
Hoeneß was instrumental in luring Heynckes's successor Guardiola to Munich and Bayern have thrived this season under the Spaniard.
Hoeneß will not start his sentence for a few weeks while the verdict is finalised with the prosecution able to appeal having wanted a longer sentence.
As a first-time offender, Hoeneß is most likely to serve his sentence in Landsberg prison, 60 kilometres east of Munich.
It is the same jail where Adolf Hitler wrote his novel 'Mein Kampf' in 1924 while serving 264 days detention for his part in the previous year's Munich Beer Hall Putsch.
A spokesperson for Munich's regional court has said Hoeness could qualify for day release after just a few weeks of his sentence.
In his absence, his successful sausage-making factory will be run by his son Florian.
Bayern's 24th German league title could be confirmed if they win at Mainz 05 and both rivals Dortmund and Schalke draw, but Hoeneß may already be behind bars.
"It's a very tough situation for FC Bayern, for Uli Hoeneß and his family," said France winger Franck Ribery following the win over Leverkusen.
"We want to keep winning for him. It's a difficult situation, but we have to keep going forward. He's a big figure and he will always be with us."