Breno was convicted of aggravated arson in 2011 and handed a sentence of three years and nine months.
However, the Bundesliga club, for whom Breno made 21 appearances, have offered him a way back into football.
The 23-year-old will be allowed to work with Bayern's young prospects, initially for five hours a day, under the supervision of the club's head of youth, Wolfgang Dremmler.
The Brazilian admitted that he had struggled in prison but was looking forward to getting involved with the club again.
"The time in prison was very hard for me," he said. "I have changed as a person and I have learned a lot in there. I am happy to be given this chance by Bayern.
"Now I can train again and later maybe play football again - this is my dream."
Club president Uli Hoeness was glad to be able to provide the Brazilian with a new challenge, but revealed that it would not be a long-term arrangement, with the player due to be deported once he is released from prison.
"We have done everything we can to give Breno this chance at Bayern," he added. "We have to thank the authorities for their excellent cooperation.
"He will be deported after his imprisonment and will try to play in Brazil."
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