The 20-year-old has been struggling with a thigh injury and has been ruled out of Saturday's clash with Bayern Munich at Wembley
The 20-year-old sustained a thigh injury during the 2-0 semi-final second-leg defeat to Real Madrid at the Bernabeu, but had been hopeful of recovering in time to feature at Wembley.
He returned to training on Tuesday but was seen grimacing and underwent scans on Wednesday to determine whether he would be fit to play on Saturday.
However, he has now been ruled out of the clash against the Bavarians and apologised to fans.
"The final was my big goal and I fought hard for this in the past weeks," he was quoted as saying on the club's official website.
"I'm incredibly sorry that I can't help the team in this crucial game. I trust our team totally and will of course be heading to London to support the lads off the field."
The Champions League final would have been Gotze's final game for Borussia Dortmund as he has already agreed a summer move to Bayern Munich.