The 20-year-old playmaker, who has scored two goals in this season’s competition, is set for a £31.5m summer move to Bundesliga rivals Bayern in the summer.
His final appearance under charismatic manager Jurgen Klopp was set to take place this weekend but Goetze has failed to overcome a hamstring injury, originally picked up in the semi-final triumph over Real Madrid last month, and will be sidelined.
“I am unbelievably sorry that I will not be able to help the team in this important match,” he said.
“The final was my big goal and in the past weeks I have battled hard for it.
“I have huge belief in our team and will naturally travel with them to London to endeavour to support the lads off the pitch.”
Dortmund, who have lifted the trophy once in their history, 1997, will have defender Lukasz Piszczek available for the final, however, the Poland international will undergo surgery on a persistant hip operation in the summer.