Aguero was withdrawn at half-time after feeling a twinge in his hamstring during the midweek Champions League loss in Barcelona.
City are still waiting to learn the full extent of the injury but an absence of two weeks would put the Argentinian out of the derby against Manchester United on March 25.
Aguero underwent a scan on his return to Manchester and results are expected at the weekend.
The 25-year-old missed five games with a hamstring injury in February but Pellegrini is hopeful the problem is not as serious this time.
Manuel Pellegrini: "Sergio will know on Saturday what he has. It is 48 hours after the exam when they will know exactly what he has.
"I really don't know, but I don't think it is really very serious. I am hopeful he will (only) be injured for a couple of weeks.
"We need to work hard with everyone, with the staff, with all the players. Now we must try to fight for the title in the Premier League."