The Latics have reached an 'Agreed Decision' with the EFL over a financial misconduct charge after being late paying players' salaries on three occasions last year.
A club statement read: "The club notified the EFL, following Football League regulations, that it was late with the payment of wages on three occasions last year - in June, July and October 2022.
"As a result, the EFL subsequently charged Wigan Athletic with misconduct for failing to comply with Regulation 64.7.
"Regulation 86 allows the EFL and a club to enter an 'Agreed Decision' where it is appropriate in the circumstances to conclude a matter effectively and equitably without referring the matter to a Disciplinary Commission."
The suspended three-point deduction is valid for 12 months with a further sanction imposed on the club's owners to deposit "an amount equal to 125 per cent of the forecast monthly wage bill in a designated club account".
Bahraini businessman Abdulrahman Al-Jasmi fronted a takeover of Wigan in 2021 after they had gone into administration in the summer of 2020.
The Latics are currently bottom of the Sky Bet Championship, four points from safety, after winning promotion as League One champions last season.