The complaint, filed in the Munich offices of the state prosecutor, is against UEFA's head of their disciplinary service Peter Limacher and his colleague Robin Boksic.
According to Bayern, the pair made comments that were "totally untrue and slanderous" in an article to appear in Stern on Thursday.
"In the edition of Stern magazine, to be published on Thursday, we read that these two people have discredited the club and individuals in professional football," read a statement issued by Bayern.
"Bayern Munich will do everything in its power to see that these people are made to account for their comments, and we have already taken appropriate measures."
The Stern report outlines how Bayern Munich was wrongly suspected of throwing their UEFA Cup semi-final match against Zenit St Petersburg in May 2008 following comments made by a Russian gangster involved in a court case.
The article claims Boksic was the source of those allegations.
At that time, German prosecutors said they had no evidence to start an investigation.
According to Stern, the UEFA employees told a Spanish prosecutor and several journalists from the magazine they had evidence of corruption linked to Bayern, but never presented any proof.
Bayern said the UEFA officials "must be sanctioned heavily" and also called on UEFA President Michel Platini to look into the matter and make a statement.