The defender lasted 38 minutes of the 3-2 win over BVB in the Champions League clash and is now a huge doubt for the La Liga showdown with Sevilla this weekend.
Varane was able to walk off the pitch, but it still looks to be a muscular injury and is the last thing Zinedine Zidane needs right now.
Real are already missing suspended trio Sergio Ramos, Dani Carvajal and Casemiro, while Cesar Vallejo is injured.
“He hurt himself and we will see. Tomorrow [Thursday] they will do a scan. The player is optimistic but he will not be available on Saturday, that’s for sure,” said Zidane.
It means midfielder Marcos Llorente may have to slot into the back four at the weekend.
“It could happen,” Zidane added. “He already knows that position. He played it for Castilla some times.”