Club receives an additional penalty for breaching the Premier League’s profitability and sustainability rules.
The deduction, announced on Monday, leaves Everton in 16th place on 27 points, two above the relegation zone.
“The independent commission heard evidence and arguments from the club on a range of potential mitigating factors for its admitted breach of 16.6 million pounds [$21m], including the impact of its two successive PSR charges,” the league said.
“The commission determined the appropriate sanction to be a two-point deduction, taking effect immediately,” it said in a statement.
Everton said it planned to appeal again.
“The club and its legal representatives have begun the preparations to appeal the commission’s decision,” it said.
“Everton remains committed to working collaboratively with the League on all matters relating to PSR but is extremely concerned by the inconsistency of different commissions in respect of points deductions applied.”
The club was charged in January for violations of the Premier League’s PSR in their financial records for a period beginning in 2019-20 and ending in 2022-23.
According to Premier League guidelines, clubs are at risk of breaching PSR if they incur more than 105 million pounds ($133m) in losses over three seasons, or 35 million pounds ($44m) annually.
The club previously admitted to a PSR breach for the assessment period ending with the 2021-22 season, having incurred 124.5 million pounds ($157m) in losses in that period, according to the independent commission.
The Merseyside club were penalized for the first breach with a deduction of 10 points in November. After an appeal, they had that penalty reduced to six points.
In a statement in January, Everton pointed out that the first charge already covered 75 percent of the time period of their second breach, for which they had already been sanctioned.
Last year, treble winners Manchester City were referred to an independent commission over more than 100 alleged breaches of finance rules, but no verdict has been reached in that case. City have denied any wrongdoing.
Everton said the Premier League did not have “a mechanism to prevent a club from being sanctioned again for breaches in financial periods that have already been subject to punishment”.
On March 31, the Merseyside club posted a loss of 89.1 million pounds ($113m) for the 2022-23 season.
While Everton were the first club to be docked points for breaching PSR, Nottingham Forest were plunged into the relegation zone this month after having four points deducted for breaking financial rules last season.
Forest are 17th with 25 points, having played one game more than Everton, and are ahead of Luton Town in 18th place on goal difference.