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.