The 20-year-old midfielder has been unable to recover from the hamstring injury he suffered during the second leg of their semi-final clash against Real Madrid.
He tried to train on Tuesday but had to quit the session before the end.
Gotze said in a statement on Dortmund's official website: "The final was my big goal and in the past weeks I have battled hard for it.
"I am unbelievably sorry that I will not be able to help the team in this important match.
"I have huge belief in our team and will naturally travel with them to London to endeavour to support the lads off the pitch."
Saturday's all-German final will be against Bundesliga champions Bayern Munich, who Gotze will join before the start of next season.
Bayern agreed to pay £37m for his services in April, making him the most expensive German footballer of all time.
Dortmund general manager Michael Zorc admitted following the latest training session: "Mario felt something again in his hamstring, which was why he stopped."