The Bavarian giants' chief believes the Brazilian's spell behind bars was unwarranted, but has vowed to continue aiding the 22-year-old's family
The 22-year-old has been sentenced to three years and nine months in prison without parole after it was ruled that he was responsible for a fire in his own villa in the Grunwald suburb of Munich in September.
He will be deported back to Brazil upon completion of his prison sentence, and Hoeness admitted that it will be very hard for the player to get his life back on track when he leaves jail.
"I do not know know if one needs really make a distinction between a bricklayer, who can carry on with his profession when he comes out again, and a young footballer, who can do absolutely nothing other than play football," the Bayern chief told Bild.
"Taking away his livelihood for all that time for this crime, which for me is unproven, is absolutely incomprehensible, in my opinion.
"A certain social hardness lies within this judgement. A sentence must punish someone, but in this case it is almost a life sentence. This is the big issue here.
"I never, ever imagined that the boy would go to prison, and moreover, for so long. If the decision is not revised, then his life is broken. For me, the verdict was a shock."
Hoeness then revealed that the club will provide for Breno's family for as long as the player is in prison, saying: "His wife is living in Germany for the time being, and our people will continue to help them.
"Whenever she has a problem that we can solve, we will do so."