Fati looked visibily upset when he was forced off in the second half and the 19-year-old will undergo further tests on Friday.
"Ansu Fati has a left thigh injury. Further tests are pending to find out the exact extent of the injury," a Barcelona statement read.
Any absence for Fati would be a considerable blow to Barcelona, who play Napoli next month in the Europa League and are battling to finish in La Liga's top four.
Fati returned earlier this month after two months out with a hamstring tear. He also came back in September following 10 months out with a serious knee injury.