The bad news for City came as Pellegrini reiterated his annoyance that having to play a key Premier League match on Sunday against Southampton might affect their European final ambitions.
Silva limped out of the first leg tie at the Etihad Stadium on Tuesday, with Pellegrini revealing: "He has a small hamstring injury and he'll need two or three weeks to recover." Asked when he might be back, he added: "He'll be able to play the final."
Yaya Toure remains another injury concern for Pellegrini following a muscle injury. "Yaya started working today, we saw the way he improved during the weekend and we'll see if he can be fit for Wednesday. At the moment we don't know."
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Pellegrini said he could not understand why, amid such a crowded schedule and with City still pushing for the top four finish that would guarantee Champions League football next season, they had not been given the chance by the Premier League to play on Saturday.
That, he had hoped, would give them an extra day to prepare for the daunting trip to the Bernabeu.
"I said this before we knew we were going to play eight games in 30 days, which is a lot for this squad, so I'm making rotations in every game we play," Pellegrini said.
"I don't understand why having so many games in this league with so much interest why we cannot play 24 hours earlier, at least the same as Real Madrid. It's not for me to say and there's a lot of things like the rights of TV, so I don't know.
"As a manager you always want to have all of the options. We're representing England and the Premier League in the Champions League. At least you don’t want to give an advantage to the other team."
Pellegrini also paid tribute to goalkeeper Joe Hart, who after his heroics against Madrid on Tuesday which enabled City to earn a goal less draw, is set to celebrate a 300th Premier League appearance on Sunday.
"He's been an important goalkeeper in the three years I've been here," Pellegrini said. "The first year he had some problems but he reacted very well, he demonstrated what a good professional he is.
"He's the number one in England without any discussion."
(Reporting by Ian Chadband, editing by Pritha Sarkar)
