Midfielder Fabregas played the full 90 minutes for Chelsea last Saturday as they beat Liverpool 2-1 at Anfield.
The former Barcelona and Arsenal man was praised for his performance by club manager Jose Mourinho, who after the match indicated that it would be a risk for Fabregas to play for Spain on Saturday due to his hamstring problem.
A medical examination on Tuesday revealed that Fabregas' condition had improved, but with the 27-year-old still said to be experiencing discomfort, Spain officials have determined that playing him at Estadio Nuevo Colombino could jeopardise his recovery.
Fabregas' place in the squad for that clash and the subsequent friendly with Germany next Tuesday has been taken by Villarreal's Bruno Soriano.
Soriano, 30, has four caps for Spain, with his last coming in the 4-1 friendly win over South Korea in May 2012.
Reigning European champions Spain sit second in Euro 2016 qualifying Group C, having taken six points from their opening three matches.
