The Spain international was substituted after 66 minutes of City's Champions League victory over CSKA Moscow at the Etihad Stadium on Tuesday.
Pellegrini, speaking at a press conference to preview this weekend's Barclays Premier League clash at Sunderland, said: "He has a problem with his calf.
"I don't exactly how many weeks it will be but maybe three or four."
Captain Vincent Kompany also remains on the sidelines with a thigh injury but Pellegrini is hopeful he will be fit for the first game after the upcoming international break.
The influential defender has missed City's last six games but Pellegrini believes he is on course for the home game against Tottenham on November 24.
Kompany was injured in the victory over Everton at Eastlands almost five weeks ago.
Pellegrini said: "Kompany had five weeks - that was the original prognosis for him. He is in his third week so he has two weeks more.
"We hope if he continues the same way he will not have any problems."
Pellegrini was unaware of reports that the Belgian Football Association was planning to send a physiotherapist to Manchester to assess Kompany.
There is general concern over the 27-year-old's fitness after a number of muscle injuries in the past two years.
"I don't know about that," Pellegrini said.
City are still without striker Stevan Jovetic due to a calf injury while midfielder Fernandinho and defender Matija Nastasic are hoping to shake off knocks ahead of Sunday's trip to the Stadium of Light.