Aguero was charged retrospectively by the Football Association after appearing to elbow West Ham's Winston Reid in the second half of Sunday's Premier League game at the Etihad Stadium.
The incident, after which Reid was seen holding his neck, was missed by referee Andre Marriner and his fellow officials during the match.
Aguero had been given until 6pm on Thursday to respond to the charge, which was issued after review a 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 home clash with Bournemouth on September 17 and EFL Cup tie at Swansea four days later are the other games he would miss.
Losing Aguero would be a big blow for City and boss Pep Guardiola, particularly with the derby meeting with Jose Mourinho's United next up.
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.
His form has helped Guardiola's side win their opening three games of the Premier League season, with United and Chelsea the only other teams in the league with perfect records so far.
Source : PA
Source: PA