Cheered on by the vast majority of the 7,000 club members at the annual general meeting and booed by a handful, Hoeness was hugged by fellow club bosses when the election result was announced.
"I want to thank you and I promise that I will not disappoint you," he told the crowd after being welcomed back by club CEO Karl-Heinz Rummenigge.
A former Bayern player and sporting director, Hoeness first became president in 2009.
He was known for voicing strong opinions and helped turn the Bavarian club into a multimillion dollar international operation.
The 64-year-old was convicted in March 2014 for evading 28.5 million euros ($31.14 million) in taxes. The 1974 World Cup winner stepped down from his post at Bayern and started his jail term in June 2014.
From early 2015, he was allowed to leave prison during the day to work in Bayern's youth department, before returning in the evening. He was released in February after serving half of his 3-1/2-year term.
Hoeness was initially charged with evading 3.5 million euros in taxes while investing millions in stocks through a Swiss bank account.
When the trial began Hoeness stunned the court by admitting he had actually evaded five times that amount -- 18.5 million euros.
That figure was subsequently raised further to 28.5 million euros -- a figure acknowledged by Hoeness's defence.
(Reporting by Karolos Grohmann; Editing by Toby Davis)
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