The diminutive Argentina international injured his knee in City’s victory over Southampton last month, while Balotelli had been suffering with sight problems after picking up conjunctivitis.
Aguero, City’s top scorer, was expecting to make a return in the middle of September but, whilst Roberto Mancini has expressed delight at his progress, he admits the 24-year-old is unlikely to feature against the Potters this weekend.
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Enigmatic striker Balotelli, meanwhile, had been having difficulty wearing contact lenses and has undergone eye surgery, but Mancini reported that the 22-year-old is back to full health.
He said: "Mario is okay - Mario now sees everything."
The 47-year-old has no fresh injury concerns ahead of City’s trip to Stoke, and could look to feature some of his new signings after a two-week break for international fixtures.
"We don't have any players with [new] injuries, we are all okay,” he added. "Always is the wrong time for the international break but we have a lot of players."