Barca prevailed 3-2 on aggregate in the semi-final tie but ended the 90 minutes at Camp Nou with nine men after Sergi Roberto and Luis Suarez were sent off.
Argentina international Mascherano completed the match but was in discomfort at the final whistle.
"The FC Barcelona medical staff have confirmed after tests carried out on Javier Mascherano that the first team player has a left thigh injury," a club statement read. "His return to action will depend on his recovery."
Although Barcelona did not put a timescale on Mascherano's recovery, a report by Mundo Deportivo said he could face two to three weeks on the sidelines – an absence that would rule him out of next Tuesday's Champions League last-16 trip to Paris Saint-Germain.