But he was deemed not fit enough to play against Crystal Palace on Saturday and was also absent at Leicester on Boxing Day, with City losing both games.
Sources close to the squad have told Goal that the Brazilian was feeling better ahead of the Leicester game, but he was not ready to join the travelling squad and a return at Southampton this coming Sunday is far from certain.
A decision will be made closer to kick-off but he is currently considered as touch-and-go to be available.
If he does miss out it would leave him short of match rhythm for City's potentially crucial meeting with Liverpool next Thursday.
Fernandinho's recent absence has been cited as a key reason in the Blues' shock defeats over the Christmas period, a run of form that has left them seven points behind Jurgen Klopp's unbeaten league leaders.
City will already be without Fabian Delph for the next three matches after he was shown a straight red card late on in the defeat at the King Power Stadium.
Benjamin Mendy is still several weeks away from a return after he underwent knee surgery in November.
In better news for Pep Guardiola, Kevin De Bruyne was fit enough to start on Wednesday while David Silva replaced the Belgian off the bench late on.
Both men are in contention to start at St Mary's on Sunday, although City staff do not expect De Bruyne to be back at the top of his game until around February, given he missed around four months of the season with two separate knee injuries.