The Argetine striker is still to recover from a knee injury and was left behind in Manchester as Pep Guardiola's side headed to Merseyside.
Guardiola was hopeful Aguero would be ready to at least make the bench at Anfield for the quarter final first leg.
But City manager confirmed his leading scorer had not been declared fit in time to make the trip.
“He is much, much better, but the physios and doctor spoke with him and he said he still wasn’t perfect.
“He is back in Manchester, I hope he will be back for Saturday.”
Aguero has been out for three weeks after picking up the injury in training.
His absence means Gabriel Jesus is set to lead City’s attack as the Premier League leaders look to win at Anfield for the first time since their Abu Dhabi takeover in 2008.
Fabian Delph is available again following a muscle injury - and Guardiola will decide on the day whether to start the England international or Aymeric Laporte at left back.
While City are without their all-time record scorer Aguero, Jurgen Klopp will miss Joel Matip and Adam Lallana.
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