The 35-year-old midfielder was only introduced as an 85th-minute substitute at the Etihad but had to be replaced by John Stones after suffering a leg injury in stoppage time.
Pep Guardiola started the night without five first-team players – with Kevin De Bruyne, Gabriel Jesus and Aymeric Laporte among those unavailable – and now faces a spell without his club captain.
“It’s bad news,” Guardiola admitted when asked about Fernandinho’s injury. “It’s a problem in his leg, I think he will be four to six weeks. It is a big blow for us because we need people there.”
The City manager had a more positive update on De Bruyne and Laporte, who both missed the Group C opener on Wednesday night with muscular issues.
“I think Kevin and Laporte start training tomorrow but I don’t know how they will be tomorrow and the next days so we will see,” Guardiola said.
“Unfortunately people came back and now we have lost another but it is really important to come back.
“In three days we go to London [to play West Ham in the Premier League] and after we travel to France to play against Marseille and then Sheffield three days after. The schedules are so demanding and we need all the players.”
Nathan Ake also missed the visit of Porto with a minor groin injury while Benjamin Mendy is not likely to return from a muscle problem until after the November international break.