The 21-year-old has made three appearances in all competitions this season, including starts in La Liga wins over Elche and Villarreal back in August.
Rafinha did not travel with the squad for the 2-0 win at Rayo Vallecano on Saturday and sustained the injury in a session for those players left behind.
"First team player Rafinha Alcantara felt pain in his thigh after Saturday morning's training session," a statement on the club's official website read.
"He is currently out of action as precautionary measure and his presence in training this week will depend on how things develop.
"Rafinha did not travel to Madrid despite being declared fit on Saturday morning."
Barcelona's next fixture comes after the international break, with Eibar set to visit Camp Nou on October 18.