The German international suffered a hamstring injury during the opening exchanges of last night's semi-final against Real Madrid in the Bernabeu.
He is expected to undergo tests later this week to determine the severity of the problem, but Dortmund manager Jurgen Klopp has conceded that it could rule the 20-year-old out for the remainder of the season.
"Mario picked up a muscle strain. It's going to be race against time for the things to come," Klopp told the club's official website.
If he fails to recover before the campaign concludes, Gotze will have played his last match for Dortmund following his decision to join German rivals Bayern Munich this summer.