Hoeness, a former Bayern player in the 1970s who also won the 1972 European championship and 1974 World Cup with Germany, was elected at the club's annual general meeting in Munich amid roaring applause.
Beckenbauer, captain of the hugely successful Bayern and Germany teams in the 1970s and who also coached Germany to their 1990 World Cup victory, becomes honorary president in a move announced a year ago.
Long regarded as the person who revolutionised football marketing in Germany when he took over in 1979, Hoeness said the club's finances were as healthy as ever.
"My successors have a golden future as we are financially independent," the 57-year-old Hoeness told the meeting. "Which other top club can claim that?"
Hoeness helped engineer the club's successful sponsorship and marketing plans as well as the construction of their 69,000-capacity Allianz Arena, which belongs to Bayern.
As a going-away present Hoeness sealed a 90 million euro deal with German car maker Audi on Thursday for the purchase of 9.09 percent of the club's shares.
