Aguero was charged retrospectively by the Football Association after appearing to elbow West Ham defender Winston Reid in the second half of City’s Premier League win at Eastlands on Sunday.
Reid was seen holding his neck after the incident, which was missed by referee Andre Marriner and his fellow officials.
Aguero had been given until 1700GMT on Thursday to respond to the charge, which was issued after a review panel felt he should have been sent off.
A date for a disciplinary hearing will now be determined.
If Aguero is found guilty he could be suspended for City’s next three domestic matches, including the derby against Manchester United at Old Trafford on September 10.
The 28-year-old would also be ruled out of City’s home league clash with Bournemouth on September 17 and an English Football League Cup tie at Swansea four days later.
Losing Aguero would be a big blow for City boss Pep Guardiola as he looks to maintain the team’s 100 percent winning start to the season.
Speaking about the incident following the West Ham match, Guardiola said he was prepared to cope if Aguero was banned.
“I didn’t see so I cannot comment,” Guardiola said of the clash.
“Hopefully nothing happens. If it happens, we accept and adapt and we will try our best.”
Aguero, who is not playing in Argentina’s forthcoming World Cup qualifying double-header against Uruguay and Venezuela due to a calf injury, has made a superb start to the season, scoring six times in his first three appearances, including a hat-trick in a Champions League play-off win at Steaua Bucharest.
