The Serie A side went out on away goals despite winning the second leg 3-2 on Tuesday after Miroslav Klose's late goal that should have been disallowed gave the German side a 2-1 advantage in the away match.
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"We are talking about being knocked out by a goal that was offside by two metres," Prandelli told a news conference. "I'm bitter."
He was proud of the way his men had acquitted themselves in European club football's premier competition this season, after they beat Liverpool twice on the way to winning five out of six of their group stage games.
"Given the spirit we have taken on the big teams with, we go out with our heads held high," he said.
"When a team loses in this way you must feel proud of what you've done and what you're doing. Winning six games out of eight is not something everyone can do.
"The lads worked and interpreted the game as we had prepared, so my work was more than satisfying."
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Fiorentina have also been hit by injuries and the loss of Romania striker Adrian Mutu, who has been given a precautionary suspension after failing drugs tests in January.
The resulting slide in form has dragged Fiorentina down to the middle of the Serie A standings, and they are unlikely to return to the Champions League next term.
"We've had emergency after emergency," Prandelli said.
Bayern coach Louis van Gaal said he sympathised with the Serie A side.
"I can understand it is hard for Fiorentina to accept being knocked out in this way. The offside goal was decisive," he said.
"It wasn't an easy match. But we played with the ball on the ground when we could in the second half and that saved us. We scored two good goals."
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