The Mexican went under the knife on Tuesday to correct a knee injury but will now face at least six months on the sidelines
The Mexico international, who has been with the club since 2002 at youth level and has a contract until 2015, picked up a cruciate knee ligament injury in training in October.
The 23-year-old went under the knife on Tuesday to correct the problem but will now face six months on the sidelines as he looks to recover full fitness by the end of the season.
Barca's official website confirmed: "Jonathan dos Santos was successfully operated on this morning, following the injury to his right knee suffered in training last month.
"Doctors Joan Carles Monllau and Ricard Pruna carried out the operation with the assistance of Egarsat.
"Dos Santos was injured in training on October 23 and is expected to be out for about six months."
Gerardo Martino's men take on AC Milan in their next clash on Wednesday November 6 at Camp Nou in the fourth game out of six of Champions League Group H.