The sanction was imposed in February and the Foxes have since dropped into the Championship relegation zone.
The club appealed against the punishment and the Premier League also lodged an appeal, arguing that further sanctions should have been imposed for late submission of the annual accounts.
But the decision has now been confirmed to uphold the six-point deduction, which keeps Gary Rowett’s side 22nd in the table and a point from safety with five games to play.
Leicester issued a statement in response to the decision, insisting they are “fully focused” on the remaining games.
The statement read: “We acknowledge that an independent Commission’s decision to recommend a six-point deduction on the club this season has been upheld by an independent Appeal Board.
“The decision relates to our profit and sustainability position for the three-year period to June 2024 and is accepted by the club.
“With the matter now at an end and five games of the season remaining, everyone at the club is fully focused on the matches in front of us and on shaping the outcome of our season through our results on the pitch.
“We know this has been a challenging period, and we thank our supporters for the backing they continue to give the team. The responsibility now is to ensure these remaining games are approached with the focus and intent our current situation demands.”
Rovers host Leicester at Ewood Park on the final day of the season. Michael O’Neill’s side are currently six points clear of the Foxes.