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."
The deduction drops Wimbledon to 18th in League Two, though they remain six points above the relegation zone with just one match to play.
Neal Eardley's side will round off their campaign with a trip to Accrington Stanley on Saturday.
