An independent commission imposed an immediate deduction which will see Everton drop from 14th in the standings into the relegation zone with four points, above bottom side Burnley on goal difference.
The club described the decision as unjust and said it would appeal.
The Premier League said it had issued a complaint against the Merseyside club and referred the case to the independent commission earlier this year.
“During the proceedings, the club admitted it was in breach of the PSRs for the period ending season 2021/22 but the extent of the breach remained in dispute,” the league said in a statement.
“The Commission determined that Everton FC’s PSR Calculation for the relevant period resulted in a loss of 124.5 million pounds, as contended by the Premier League, which exceeded the threshold of 105 million pounds permitted under the PSRs.”
Everton’s most recent figures showed a fifth straight year of losses, with their total loss over that period amounting to over 430 million pounds ($534 million).
The club said they had posted a loss of 44.7 million pounds for the 2021-22 season earlier this year.
The Premier League said one of the factors that aggravated Everton’s default was over-spending on players despite repeated warnings.
Everon invested nearly 750 million euros in transfers to build the squad since the 2016-17 season. The club was taken over by British-Iranian billionaire Farhad Moshiri in 2016.
“The commission considers that it was unwise for Everton not to have curtailed player purchases,” it added.
“It was aware of potential PSR difficulties but pressed ahead in the hope that it would make sales of players that would enable it to achieve PSR compliance. Events have proved that to be a poor judgment.”
Everton said the sanction was “wholly disproportionate and unjust” and announced its intention to appeal the decision to the Premier League.
“Everton maintains that it has been open and transparent in the information it has provided to the Premier League and that it has always respected the integrity of the process,” it said.
“Both the harshness and severity of the sanction imposed by the Commission are neither a fair nor a reasonable reflection of the evidence submitted.”
Everton were sold to 777 Partners in September in a deal reports said was worth more than 550 million pounds, with the company acquiring Moshiri’s 94.1% stake in the club. The deal is expected to be closed by the end of the year.
Earlier this year, Manchester City were also referred to an independent commission over more than 100 alleged breaches of finance rules since the club were acquired by the Abu Dhabi-based City Football Group. No verdict has been reached in that case.