The midfielder suffered a knock in the defeat to Manchester United last weekend and hasn’t trained since.
But Pep Guardiola says he will wait until Saturday's training session at the CFA before making a decision on his involvement at the Emirates.
“David Silva is not fit,” he said. “Tomorrow we'll see.
“Yesterday and today he could not train. It was a kick in some part of the leg that is painful.
“It’s not a big issue.”
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Stones limped out of the Manchester derby last weekend with a hamstring problem and missed the midweek win over Dinamo Zagreb, while Aguero hasn’t played since the win over Chelsea due to a muscular injury.
And Guardiola has confirmed neither will play any part in Sunday's big game.
No [Stones is not fit],” he said. “He has a muscular injury and don’t know when he will be back.
“Aguero still doesn’t train with the team.
“The players who were injured are still injured, the players who play in Zagreb are okay. They train good today.”