The team from Bavaria, a leading global football brand, played a friendly against Al-Hilal in Riyadh on Saturday in a one-day trip organised by a club sponsor.
It coincided with an uproar over the flogging in Saudi Arabia of activist and blogger Raif Badawi and Zwanziger accused Bayern of being driven by "commercial ethics".
"If Dr Theo Zwanziger has indeed forgotten what he once said (about Bayern) then we are seriously worried," read a column on the club website. "Does the Dr need a doctor?".
"Dr Theo Zwanziger ... is grateful to have used his chance at Bayern's expense to hit the headlines."
The club also said Zwanziger, during his time as head of the German FA (DFB), had repeatedly praised them and listed a number of his quotes from the past.
The Bavarians added that Germany, when Zwanziger was on the DFB board, played in Saudi Arabia in 1998 but that never caused any problems.
Zwanziger believed the club should not have played in Saudi Arabia.
"I know commercial ethics has ruled at Bayern for some time and when in any doubt they always side with the money bag. It is a shame but it does not surprise me," he said.
(Reporting by Karolos Grohmann, editing by Tony Jimenez)
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