The striker picked up an injury in training and sat out his sides 2-1 victory in Watford in midweek and joins former Blues midfielder Kevin De Bruyne on City's injury list.
De Bruyne has missed the champions' last month of fixtures after damaging knee ligaments in the Carabao Cup win over Fulham.
Speaking in today's press conference, Pep Guardiola confirmed both stars will be unavailable for tomorrow's clash against Chelsea but they will be back "soon."
The City boss said: "Tomorrow is another huge demanding test for us. How will they react after losing? I can imagine how intense, committed they will be.
"I have been to Stamford Bridge many times and I have won once, last season; always I lose there.
"They are a good side, a really good team. When you see the XI and the people on the bench, they are a real contender."
City and Liverpool remain the only two unbeaten sides in the Premier League season but Guardiola has dismissed claims his side could match the invincibles.
He said: "I don’t care about that. It’s just the next game, to try to win the game, to play good.
"I am proud that we have been consistent for 15/16 months over three days. It’s a big compliment for the players.
"They know it and I tell them every day but in the last game we could have dropped two points in the last ten minutes. There are many things we could do better.
Liverpool will go top for at least a few hours if they win at Bournemouth meaning City will most likely have to avoid any slips up at Stamford Bridge.
Gabriel Jesus is likely to once again lead the line in Aguero's absence but the 21-year-old Brazilian has struggled in front of goal this season, with just one goal in 12 appearances.
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