The 26-year-old was brought off in the 82nd minute of the game and was sent for scans to discover the extent of the damage.
The scans revealed that he had sprained his ligament and Barca have contacted the Spanish FA to recommend that the midfielder does not travel for the game.
A statement on the club's official website said: "Cesc Fabregas had a number of tests this morning after arriving back from Malaysia to measure the extent of the ankle injury he picked up in Saturday's match.
"It has subsequently been confirmed that the player has sprained a ligament in his right ankle.
"Club doctors have contacted the Spanish FA to recommend that the player should not join the national squad for the friendly against Ecuador so that he can undergo treatment in Barcelona."
Fabregas, who has been the subject of interest from Manchester United this summer, now faces a race to be fit in time for the opening game of the season.