Hoeness, who replaced Franz Beckenbauer after stepping up from his role of director of sport in 2009, received 97% of the votes, earning resounding confirmation of his work over the past two seasons, even if he was unable to produce any trophies.
"It's a dream to be president of this club," said Hoeness.
Record profits were also announced at the AGM as Bayern contradicted an economic crisis with a 20th straight profit-making financial year.
"I think the members of Bayern Munich can be proud of these results," said the club's board member Kar Hopfner, who unveiled a record turnover of 373.4 million euros for a profit of 11.1 million euros, compared to 1.3 made in the previous financial year.
Bayern are also proving to be profitable on the field as they head into a Bavarian derby at Nuremberg tomorrow [Saturday] with an astonishing 30 points from 11 games.
Only Bayer Leverkusen have taken anything off the record German champions, who will aim to continue their push towards a first piece of silverware in three years at the Frankenstadion.
They now have an extra ace in the pack too with Germany international Mario Gomez making his comeback from injury in a friendly match in midweek, giving coach Jupp Heynckes a selection headache with Mario Mandzukic and Claudio Pizarro also showing good form of late.
"Everybody is number one here because we have top strikers," said Heynckes.
An immediate return to the starting XI is unlikely for Gomez, who has been out since August 5.
"It's my job to build him up gradually and carefully," Heynckes said. "I want to see how the foot copes. I have a duty to his health."
Nurnberg coach Dieter Hecking's job this week has been to build up his own side and give them belief that they can decide the 185th Bavarian derby for themselves.
"We don't need to make ourselves out to be small," he said "I would like my team to see that they have a chance, and then to take it.
"Games between us have always been tight and I have the courage to say we are going to challenge Bayern."
Goalkeeper Raphael Schafer returns for Nurnberg while Markus Feulner should replace the suspended Hanno Balitsch in midfield.