The former West Germany international was put behind bars for three and a half years after being found guilty of tax evasion last week.
The 43-year-old Guardiola has already voiced his sadness that his "friend" will no longer be at the club and is willing to wait until his jail term ends.
"I'll continue until Hoeness comes back," the former Barcelona coach is quoted as saying by Mundo Deportivo. "I want to do my best for the club. I want to continue working here for two or thee years. My dream is to be here when he returns.
"Without Hoeness all this would not have been possible."
Guardiola's current contract at Bayern expires in the summer of 2016.