The punishment comes for including six loan players in their squad for the defeat at Burnley on November 28 but £1,000 of the fine has been suspended.
Under Football League rules, the maximum number allowed to feature on the match-day team sheet is five.
Goalkeepers Graham Stack (Reading) and Tony Warner (Fulham), defenders Matt Heath (Coventry) and Ugo Ehiogu (Middlesbrough) and strikers Geoff Horsfield (Sheffield United) and Tresor Kandol (Barnet) were all included in Dennis Wise's squad for the 2-1 defeat at Turf Moor.
In mitigation, Leeds pointed out that their central defender Matthew Kilgallon had been a last-minute withdrawal from the squad due to an ankle injury.