The Germany international picked up a knock in the opening stages of BVB's 2-0 Champions League loss against Real Madrid on Tuesday and limped off the pitch after only 14 minutes of play.
It's not yet known exactly how long the 20-year-old will be out of action due to the injury, but Klopp believes Gotze could face a race against time in order to be match fit in time for the Champions League final on May 25.
"Mario picked up a muscle strain. It's going to be race against time for the things to come," Klopp was quoted as saying on the club's official website.
Gotze is expected to undergo a series of tests once Dortmund returns to Germany after Tuesday's match at the Santiago Bernabeu.
The attacking midfielder will certainly miss this weekend's Bundesliga game at home against Bayern.