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Goezte, 20, tore his right hamstring in Dortmund's semi-final return leg at Real Madrid on April 30 and the attacking midfielder only managed an hour of training with the Borussia team on Tuesday before suffering a reaction, which has ruled him out.
"It was my big aim to play in the final and I have been working hard to reach that in the last few weeks," said a disappointed Goetze on Wednesday.
"I am incredibly sorry that I can't help the team in this really important game.
"I have full confidence in the team and will of course be going to London to support the boys from the sidelines."
His withdrawal means Goetze has now played his last game in a Dortmund shirt after it was announced in April that he will join German champions Bayern for €37 million.
Meanwhile, Dortmund are waiting on the fitness of centre-back Mats Hummels, 24, who damaged his ankle in Saturday's shock 2-1 league defeat at home to Hoffenheim, and sat out Tuesday's training to allow the swelling to subside and is receiving intense treatment.
