At the conclusion of a four-day trial in Munich, the 62-year-old was condemned to a three-and-a-half year term for failing to declare 28.462 million euros in due taxes.
Wolfgang Niersbach told Munich's Abendzeitung newspaper: "The whole dimension this case has taken on in the past few days even surprised us at the DFB.
"The great achievements of Uli Hoeness for Bayern Munich and for the whole of German football will not be affected by this process.
"The legal judgment in such a case must be taken by the courts and the same rules apply to Uli Hoeness as to anybody else."
The Bavarian State Prosecutors took the view that Hoeness' reporting himself for tax evasion did not make him immune from punishment.
In February last year, Hoeness approached the German tax authorities, admitting he had withheld sums in a foreign account.
Hoeness paid the unpaid taxes, but the total amount he evaded increased from the amount he had declared - 3.5 million euros - to 28.462 million. The defendants did not contest this figure.
Hoeness' sentence will only be legally binding at the end of the appeals process. His defence solicitor Hanns Feigen announced they would be making an appeal, meaningHoeness remains a free man for the time being.
Hoeness has been with Bayern since penning a professional playing contract in 1970.
After ending his playing career due to injury in 1979, he moved into a managerial role at the club, becoming the youngest general manager of a Bundesliga club in the history of German football.
He held that position for 30 years before being elected club president in 2009 after Franz Beckenbauer stepped down, becoming honorary president.
His future with the Bavarian club is due to be discussed at board level on Friday.