The Dons selected Jake Nicholson in the matchday squad for their Sky Bet League Two clash with Cheltenham on March 22 and he came on as a substitute at half-time, scoring as they went on to win 4-3.
Following a Football Disciplinary Commission on Monday, they have been docked three points and fined £5,000, suspended until the end of next season.
The deduction sees Neal Ardley's side drop from 14th to 18th in the table, but they are not in danger of relegation with only one game to play.
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 March 22.
"AFC Wimbledon won the match 4-3 with Nicholson coming on as a substitute at half-time, before scoring his side's second goal in the 70th minute.
"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."
Source : PA