The Croatian striker's future at the club now appears to be in serious doubt with Robert Lewandowski joining the club in the summer on a free transfer from Saturday's opponents.
Pep Guardiola confirmed the 27-year-old had been injured recently but that was not why he was left out of the squad.
"He was injured, but on the other hand he actually was able to play," Guardiola said.
"But I decided to take 18 players with me. And Mandzukic is not in the squad."
The Daily Mirror reported earlier on Friday that Chelsea are ready to offer Bayern David Luiz as part of a deal to land Mandzukic
Sport Bild in Germany tweeted that Guardiola had already said goodbye (forever) to Mandzukic on Thursday.
The latest developments contradict quotes from Bayern sporting director Matthias Sammer last month when he said Mandzukic was an 'animal' and that "nobody even has to bother making an approach for" him.
Mandzukic has scored 26 goals for Bayern this season in all competitions, including 18 in the Bundesliga.
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