The Italian striker has fallen out of favour under Louis van Gaal at Allianz Arena and has expressed his interest in departing the club in the winter transfer market.
Beckenbauer admits he would like to hold on to Toni but concedes an exit is inevitable.
"I like Toni as a player and as a person. He has done a lot in Munich and Bayern have given a lot to him," the Germany legend told Gazzetta dello Sport.
"I would like to keep him but if he wants to go then he should go."