Fabregas, who has been the main transfer target of Barclays Premier League champions Manchester United this summer, left the pitch after a crunching challenge 10 minutes before the end of Barca's 3-1 friendly win over a Malaysia XI yesterday.
A statement on Barcelona's 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 is one of five Barca players called up by Spain coach Vicente Del Bosque for the friendly against Ecuador.