City were charged in August and pleaded guilty during a hearing on Monday.
The deduction, effective immediately, will see Garry Monk's team drop five places to 18th in the second-tier with 41 points and they could face a potential relegation battle with eight matches remaining this season.
"The Profitability and Sustainability Rules, aligned with those in the Premier League, became effective in 2015-16," an EFL spokesman said.
"Season 2017-18 was the end of the first full reporting period with Birmingham the only club found to have breached those requirements, when it incurred adjusted losses of 48.787 million pounds.
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"The disciplinary commission had the opportunity to consider all relevant factors in reaching its determination, including the club's mitigation."
The EFL said that the change to the Championship table was subject to the outcome of any appeal. The parties have 14 days to appeal the decision.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Christian Radnedge)
