The Paraguay international was caught on television footage spitting at Wolves captain Richard Stearman in the Latics 3-1 defeat to the Molineux club on Sunday.
Despite no action being taken by referee Lee Probert at the time, the FA charged the South American with indiscipline, and gave him to 6pm on Tuesday to appeal.
However, the side from the DW Stadium have released a statement clarifying that Alcaraz accepts the charges, and that he may well get more punishment after an internal investigation.
“Paraguay defender Antolin Alcaraz has accepted the FA’s misconduct charge for spitting following the incident at the end of Sunday’s Premier League match against Wolves, which carries an automatic three-match ban,” a Wigan statement read.
“The matter will be treated with the utmost seriousness and be dealt with internally, according to the club’s code of conduct.”
The suspension means that Alcaraz will miss the games against Blackburn, Sunderland and Arsenal, and will only be eligible again for the fixture with West Brom at the Hawthorns on 10th December.
By Gareth McKnight