The midfielder was forced off in the first half at the Etihad Stadium and replaced by fellow Brazilian Fernandinho.
City boss Manuel Pellegrini revealed after the game that Fernando was set for further assessment.
"Fernando has a muscle problem in his groin," said the Chilean.
"We will see tomorrow [Sunday] with the doctor how strong it is."
A break for international fixtures means City are not in action again until September 13, when they visit Arsenal.
The champions suffered their first defeat of the season against Stoke, with a fine solo goal from Mame Biram Diouf earning a shock victory for Mark Hughes' men.
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