City's 19-year-old Nigerian striker Kelechi Iheanacho scored twice, in the 64th and 74th minutes, and was brought down for the penalty in the 43rd minute from which Sergio Aguero scored has 16th goal in as many games this year.
Fernando headed City's opener from Jesus Navas's 35th-minute corner. Stoke have now conceded four goals in each of their last three games.
Iheanacho will be hoping to retain his starting slot for City's Champions League semi-final first-leg game against Real Madrid at the Etihad on Tuesday.
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(Reporting by Neil Robinson, editing by Ed Osmond)
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