Dortmund confirmed Wednesday that Goetze will not be fit in time to face his future club at Wembley Stadium in London. It would have been the 20-year-old Goetze's last game for Dortmund before his 37-million euro switch to Bayern next season.
"The final was my main aim and I fought hard for it in the last weeks," Goetze said on Dortmund's website.
Goetze returned to training on Tuesday but suffered a recurrence of the problems that forced him off in the semifinal second leg against Real Madrid on April 30. After completing an individual jogging exercise in the morning, he broke off training after an hour with teammates in the afternoon.
"I'm incredibly sorry that I can't help the team in this important match," Goetze said. "I have full confidence in our team and will of course travel with the side to London to support the lads from the side of the pitch."
It will be the second Dortmund final against Bayern that Goetze will have to watch from the sidelines. The attacking midfielder missed most of the second half of last season with a thigh injury and could only watch from the bench as his teammates routed Bayern 5-2 in the German Cup final.
Dortmund coach Juergen Klopp will now likely turn to Germany teammate Ilkay Gundogan to take Goetze's position behind Polish striker Robert Lewandowski.
"I don't think it's that difficult. I played there in the youth teams and know what's required of the position. I know what I have to do," Gundogan said last week.
Klopp also has the option of bringing Marco Reus into the centre, where the Germany international played in the 2-1 Bundesliga loss to Hoffenheim last Saturday, with Kevin Grosskreutz coming in on the wing to help left back Marcel Schmelzer cope with Bayern's Arjen Robben and Philipp Lahm.