The 20-year-old lasted just 14 minutes against Real Madrid before being forced off with an apparent hamstring tear.
And Dortmund coach Jurgen Klopp has confirmed the midfielder will be facing a fight to be fit for the May 25 Wembley final.
"It's going to be race against time for the things to come," he said.
Dortmund held on to book their place in the final despite a 2-0 defeat in the second leg of their semi-final, progressing 4-3 on aggregate.
Gotze, who will join Bayern Munich this summer, has emerged as one of the most coveted players in European football since coming through the ranks at Dortmund, and his absence would be a real blow to Klopp's side as they look to clinch their second Champions League title.
Meanwhile chairman of the Bundesliga outfit, Hans-Joachim Watzke, admitted he could not bear to watch the remaining minutes at the Bernabeu.
"It seems like we only can do it with drama," he said.
"For the first time in my life I had to give up due to heart problems. I went to the toilet for the last minutes, locked myself in, covered my ears and looked at my watch. I had all kinds of thoughts going through my head."