The 64-year-old's first stint as president ended when he was convicted of tax fraud in 2014 and the former Bayern forward served nearly two years of a three-and-a-half-year sentence before being released on February 29 this year.
He was the only candidate to stand for the post at Friday's annual general meeting and will succeed Karl Hopfner, who stepped into the role after Hoeness' imprisonment.
Chief executive Karl-Heinz Rummenigge had said before the election: "Dear Uli, I wish you a beautiful, successful and emotional return to your old post as FC Bayern president.
"I'll never forget your face and your eyes when you came back to the Sabener Strasse (Bayern's training centre) for the first time on 2 January, 2015.
"I'm looking forward to working with you again. I wish for a trusting, loyal, harmonious, respectful and good cooperation for the benefit of FC Bayern. Dear Uli, welcome back."