The Argentine striker elbowed West Ham United defender Winston Reid during Sunday's Premier League match at the Etihad Stadium, which City won 3-1.
He will be unavailable for the derby at rivals Manchester United on Sept. 10 and will also miss City's Premier League clash with Bournemouth and a League Cup third-round tie against Swansea City.
"Sergio Aguero will serve a three-match suspension with immediate effect after an FA charge of violent conduct against him was found proven," the FA said in a statement on its website.
"The club denied the charge and submitted further that, if it was to be found proven, the standard punishment would be clearly excessive.
"On finding the charge proven at a hearing today (Friday 2 September 2016), an Independent Regulatory Commission went on to reject the club's further claim to decrease the three-match ban."
Aguero has scored in two of City's three league games so far this season, and also grabbed a hat-trick against Steaua Bucharest in a Champions League playoff match on Aug. 16.
He has missed Argentina's World Cup qualifiers against Uruguay on Thursday and Venezuela next Tuesday with a calf muscle injury.
(Reporting by Simon Jennings in Bengaluru; Editing by Rex Gowar)
