The 61-year-old received an overwhelming majority of 99.6 per cent of votes to replace Uli Hoeness at the helm of the club, with Rudolf Schels becoming vice-president
Former president Hoeness stepped down from the post in March after being sentenced to three-and-a-half-years in prison for tax evasion.
Bayern called an extraordinary general meeting on Friday to determine who would succeed the 62-year-old, and have since announced that Hopfner - the former senior vice-president - will take up the post having received a massive majority of 99.6 per cent of the votes, while Rudolf Schels has moved into the senior vice-president role.
"Thank you for your tremendous confidence," he told assembled shareholders and reporters. "I will take up the post with heart, passion and soul, as I have done for over 31 years in various positions.
"I am proud to be part of the Bayern family and will always look to work for the benefit of FC Bayern Munich."
Hopfner became deputy chairman for Bayern's executive board in 2002 having previously held the post of managing director from 1983 until the mid 1990s. He was widely praised for his work on stabilising the club's finances during his initial years with the club.
The 61-year-old also sits on Uefa's club committee and has worked closely with the German Football Association.
Hoeness is expected to return to a position at the club once his term in prison has been served.