Fernandinho is facing four to six weeks out of action after suffering a leg injury in Wednesday's Champions League victory over Porto.
Pep Guardiola confirmed the midfielder's expected lay-off in his post-match news conference following City's 3-1 win.
Fernandinho came on as an 85th-minute substitute but had to be replaced in stoppage time by John Stones.
The Brazilian is the latest injury concern for Guardiola, who was already without Kevin De Bruyne, Gabriel Jesus, Aymeric Laporte and Benjamin Mendy.
Ruben Dias and Eric Garcia started at the back for City on Wednesday, while Nathan Ake - who featured alongside Dias in Saturday's win over Arsenal - was deemed unfit to play against the Portuguese champions after suffering with "niggles in the groin", according to Guardiola.
The Champions League has proven a frustrating competition for Guardiola and his side had to come from behind in the opening game of this year's group stages.
Luis Díaz had put Porto in front after 14 minutes, but City responded to the early setback within a few minutes when Sergio Aguero scored his first goal in 231 days when converting from the penalty spot (21) after Pepe fouled Raheem Sterling.
A sublime free-kick from Ilkay Gundogan and fine finish from substitute Ferran Torres completed the turnaround for City, who go top of the early standings in Group C.
Elsewhere in the group, Olympiakos scored a stoppage-time winner to beat French side Marseille at home.
Pep aims to convince Garcia to sign new City deal
Guardiola also said he hopes to convince Spain international Eric Garcia to extend his contract at the Etihad Stadium.
City rejected a Deadline Day bid worth £15.4m plus add-ons from Barcelona for Garcia, who is in the final year of his contract at the club.
"I know he wanted to leave but he's going to stay and maybe we can seduce him in this year to extend the contract with us," Guardiola said of the 19-year-old former Barcelona academy product.
"He's a guy who is so stable in many things and we're so happy."