The Argentina international had cancelled out Ross Barkley's stunning opener but pulled up after his equaliser and was replaced after just 28 minutes
The Argentina international had equalised for City after Ross Barkley's stunning opener but pulled up shortly after his goal.
Aguero attempted to play on but could not continue and was subsequently replaced by Fernandinho in the 28th minute.
The 25-year-old has scored 28 goals in 33 appearances for City this term but his campaign has been disrupted by calf and hamstring injuries.
Manuel Pellegrini's side require a win at Goodison Park in order to pull level on points with Premier League leaders Liverpool, who play their penultimate game of the season against Crystal Palace on Monday.