Mandzukic has been linked to a hosts of Premier League clubs including Chelsea and has met with Bayern Munich's CEO Karl-Heinz Rummenigge in May to confirm his unclear future at the club.
"At Bayern it was fantastic. It's a fantastic club. Indeed, until recently I didn't even think about leaving, and especially that it would happen now.
"Let's be honest, the style Guardiola wants at Bayern doesn't suit me.
"In the first leg against Real in Madrid (in the UEFA Champions League), I definitely understood, no matter how much I try, I can't get the best out of myself with this style.
"When it's like that, I don't feel good and it's best for everyone that we part.
"Thanks to the club who offered a contract extension, thanks to Guardiola, who is a great coach, and I wish everyone all the best for the future.
"Bayern and their fans will always be the most beautiful and most emotional story of my career. The time has come for new challenges."
Mandzukic, who will be representing Croatia at the World Cup finals in Brazil, has refused to reveal his next destination.
However, Mandzukic will be suspended against Brazil in the tournament's opening match on June 12 but will be available for Croatia in the other group's fixtures.
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