City manager Pep Guardiola has confirmed the club's all-time leading scorer did not travel with the rest of the squad to Merseyside ahead of Wednesday's game at Anfield.
The forward has instead remained in Manchester to undergo further treatment on a problem he picked up in training prior to the international break.
However, Guardiola refused to rule the player out of contention for the derby with Manchester United, with City knowing a win over the neighbours on Saturday will secure the Premier League title.
"He's in Manchester, he didn't come. He's still not fit," Guardiola told the media.
"We'll see [about the derby]. He's much, much better, but he spoke with the doctors and he was still a little bit uncomfortable."
With Aguero absent, Gabriel Jesus is set to start in attack against a Liverpool side who remain the only team to beat City in the league this season.