Aguero has until 18:00 BST on Thursday 1 September to respond to the charge.
If found guilty, the Argentina international faces a three-match ban.
He would miss Premier League games with Manchester United on 10 September and Bournemouth on 17 September.
The 28-year-old would also miss the EFL Cup third-round game against Swansea.
Referee Andre Marriner did not see the 76th-minute incident during City's 3-1 win on Sunday and the FA has decided to take retrospective action after reviewing television footage.
Aguero is currently out of Argentina's two World Cup 2018 qualifiers next month with a calf injury.

He is currently director of the University of Toronto's Munk School of Global Affairs.
The Canadian academic, with an expertise in international law, was a postgraduate student at Cambridge in the 1980s.
Prof Toope will take over in October 2017, when the current vice-chancellor, Sir Leszek Borysiewicz, steps down.
The new Cambridge head, whose appointment will have to be approved by the university's governing body, is a former vice-chancellor of the University of British Columbia.
His academic work has specialised in human rights and international dispute resolution, and he has worked for the UN Working Group on Enforced or Involuntary Disappearances.
Prof Toope will be the 346th person to hold the office, in a role dating back to 1412.
He said: "I am thrilled to be returning to this great university.
"I look forward to working with staff and students in the pursuit of academic excellence and tremendous international engagement."

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Rose, 36, held a two-shot lead with five holes to go but lost when Garcia birdied the first extra hole on Sunday.
He had a one-shot lead on the 17th but made bogey and both parred the last.
"I feel it is a tournament I can still do well in, said Rose. "It's a course you can get to know and be competitive here for a long, long time."
Rose, who has finished tied second, 10th and second in his last three Masters, was referring to 57-year-old American Fred Couples, winner of the Green Jacket in 1992, who has had six top-20 finishes in his last seven appearances.
"I see myself having many more chances to come," the world number 14 told BBC Sport.
Rose claimed his only major win at the US Open in 2013 but was in the clubhouse at Merion as contender Phil Mickelson finished his round.
At Augusta, where he has now finished in the top 10 on five occasions, he was alongside Garcia in the final pairing as the pair wrestled to land the first major of the season.
Rose fought back after Garcia had taken a three-shot lead early on and appeared to have control with five to play, only for the Spaniard to follow birdie on 14 with what was his first eagle at Augusta in 452 holes, ending a wait dating back to 2011.
Both men missed putts for birdie when at nine under par on 18 before Garcia landed his first major in the play-off.
"I felt in control all day," added Rose. "Sometimes the rub of the green is for you and sometimes it isn't. I hit a really good putt on 18 in regulation and thought it was going in.
"I am really happy for Sergio. I would love to be wearing the Green Jacket but if it wasn't me I am glad it is him.
"We have been friends for a long time and playing golf against each other since we were 14 years old. We will get up and he will be happy for a month and then golf will take over, I will be unhappy for a month and golf will take over for me."
Manchester City striker Sergio Aguero has been given an extra 24 hours to argue his case after being charged with violent conduct by the Football Association for elbowing West Ham's Winston Reid.
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Stephen Toope has been chosen as the next vice-chancellor of the University of Cambridge.
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Masters runner-up Justin Rose believes he will have "many more chances" to win at Augusta National in the wake of his play-off defeat by Sergio Garcia.