The club have been punished for fielding Jake Nicholson, a midfielder signed from Greenock Morton in February, against Cheltenham Town in a 4-3 win at Kingsmeadow.
Nicholson was introduced as a half-time substitute and went on to score as Wimbledon came from two goals down to secure victory.
A Football League statement read: "A Football Disciplinary Commission has ruled that AFC Wimbledon are to be deducted three points for fielding an ineligible player, Jake Nicholson, in the Sky Bet League 2 fixture with Cheltenham Town on 22nd March.
"The club were also fined the sum of £5,000, suspended until the end of the 2014-15 season, and must pay the costs of the hearing."
Neal Eardley's side will round off their campaign with a trip to Accrington Stanley on Saturday.
