The return of all the points would have seen the club - who have already sealed a play-off spot in League One - secure automatic promotion.
However following a lengthy hearing, the three-man arbitration panel ruled the league had not acted unfairly when docking the points.
Earlier in the day, Leeds chairman Ken Bates revealed he would accept the decision of the panel.
"The matter is now closed and the focus can now return to the pitch," read a club statement.
"If the team are now able to progress through the play-offs to the Championship, then it would be the appropriate reward for the efforts of the club's fans and players in overcoming the penalty imposed."