An appeals panel has upheld the penalty imposed on Bolton over their failure to fulfil fixtures after the EFL had challenged it for being too lenient.
The disciplinary commission ruled in November that Wanderers should face a five-point deduction, suspended for 18 months, plus a fine.
The EFL announced on Tuesday that an arbitration panel had ruled that the original sanction was sufficient.
The club, who faced major financial issues before the completion of a takeover in August, did not fulfil a Championship fixture against Brentford last season or a League One game against Doncaster in August.
The original sanction included fines of £20,000 and £50,000 for the non-fulfilment of those matches, with half of the total amount also suspended for 18 months.
A statement from the league read: "While disappointed with the verdict, the EFL respects the decision taken.
"Discussions will now continue with EFL clubs to formalise a scale of sporting sanctions for breaches of relevant EFL regulations, relating to non-payment of debts and non-fulfilment of fixtures, in future."
Bolton Wanderers' Chairman, Sharon Brittan, said: "We are pleased that this decision brings to an end the uncertainty regarding the original conclusion of the Disciplinary Commission.
"The case was one of the major legacy issues we inherited at the Club and we welcome the opportunity to be able to move forward.
"Our attention can now be completely focused on the pitch as we strive to retain our status in Sky Bet League One."