Pep Guardiola confirmed Aguero is still to recover from the thigh injury that has sidelined the Argentine in recent weeks, while Stones is also out with a muscular issue.
The Premier League champions have no other fresh injury concerns ahead of the game at the Emirates as City aim to bounce back from the derby defeat to Manchester United.
Stones’ injury means Nicolas Otamendi is likely to partner Fernandinho in central defense, while Gabriel Jesus is set to lead the attack after his hat-trick against Dinamo Zagreb in the Champions League.
Guardiola said: “Stones has got a muscular injury – I don’t know how long it will be. Sergio still hasn’t trained with the team. The players who are injured are still out. The others who played in Zagreb trained good today.”
David Silva will face tests over the weekend to see if he can recover from the knock he picked up against United.
“He’s not fit,” added Guardiola. “Yesterday and today he couldn’t train, then we’ll see tomorrow. It was a kick on the leg that was painful. It is not a big issue.”
Guardiola wouldn’t confirm if Phil Foden will keep his place after an outstanding performance in the Champions League – but defended his development of the 19-year-old.
He added: “He played 50 games and he’s 19 years old, in one of the top teams in Europe. I don’t know if there’s anyone of his age who’s played that many games.
“We’re delighted with him and he’ll make incredible games in the future. I’m so happy with the way he played, an incredible experience for him, help every training session. Maybe not all 50 games are 90 minutes, but he’s been involved in difficult moments, Tottenham last season, Atalanta.
“We trust a lot with him. Sometimes he doesn’t play but it’s for good reasons; Kevin (De Bruyne), David (Silva) and Bernardo can play there. Every season he’s playing more minutes and one day he’ll be a player who will play every weekend, we’ll see when.”