Aguero had been out for a month prior to last week's Manchester derby, in which he emerged from the bench and appeared to be fouled by Manchester United's Ashley Young late on - only for referee Martin Atkinson to wave away penalty appeals.
And manager Pep Guardiola says the Argentina forward could not train after that incident, but pushed himself in an unsuccessful attempt to rescue City's European campaign in the final 24 minutes of the second leg against Liverpool.
"Aguero is injured - he was injured before the game, that was why he did not start," Guardiola told a pre-match news conference. "He was not ready."
Adding that John Stones will join Aguero in sitting out against Spurs, Guardiola continued: "I don't know [when Aguero will be back]. We cannot forget he had a month injured.
"He made a huge effort, because after the action from Ashley Young against United he had problems in his knee. He could not train. He played the last 15 or 20 minutes and, after the game, he said 'I could not run, I cannot play'.
"For Swansea [City, after Tottenham], I do not know if he will be ready. Hopefully [he will be back] for the last games, if we need him, and especially for the World Cup."
And Guardiola is expecting a tough test against Tottenham as City look to bounce back from three straight defeats in all competitions.
"They are a fantastic team with great players," he said. "They do great pressing and have a lot of talented players, like [Mousa] Dembele, [Jan] Vertonghen, Dele Alli, [Christian] Eriksen, Son [Heung-min] and [Harry] Kane is their top scorer.
"They have played great in the last two or three seasons with great success and they are already in the FA Cup semi-finals. It is going to be difficult for us."