Bolton's rearranged Championship game against Brentford planned for 7 May will now not take place and the Bees will get three points for a 1-0 win.
The match was scheduled to take place on Saturday, 27 April but was called off 16 hours before kick-off as players refused to play over unpaid wages.
Unable to confirm that adequate safety personnel will be in place next week, Bolton were given a prohibition notice.
The EFL said Bolton were now guilty of misconduct and will be disciplined.
"Following the decision taken by Bolton Wanderers' Safety Advisory Group (SAG) to issue a prohibition notice preventing Tuesday's rearranged fixture with Brentford from taking place, the EFL will not be asking that the game is played at a future date," an English Football League statement said.
"There is no provision under EFL regulations to direct clubs to play at a later date than four days past the conclusion of the season and, as a result, it has been determined that Brentford will be awarded the three points on the basis of a 1-0 victory.
"As a consequence, Bolton Wanderers is now deemed to be guilty of misconduct by the EFL which will result in disciplinary proceedings against the club being taken at an appropriate time."
Bolton, who have already been relegated from the Championship to League One, were initially told that they must complete the fixture "at the earliest opportunity".
The EFL had said that it was "satisfied that a team can be selected from the players they have registered and available to them" for their remaining two league fixtures, even if first-team players did not make themselves available for selection.
Sunday's game away at Nottingham Forest will go ahead as planned after the squad made themselves available to play in that match.
BBC Sport understands the PFA agreed to loan the club money to cover part of the unpaid wages earlier this week, although defender Andy Taylor told BBC Radio 5 Live on Friday that they still have not received any payments towards their outstanding wages for March and April.
Despite the Brentford home fixture being rearranged for Tuesday, 7 May - two days after the season ends - the EFL made the decision to call the match off altogether and award the Bees victory in the process.
Brentford's three points move the west London club up three places to 12th in the table before their final-day fixture at home to Preston on Sunday (12:30 BST).
"I think it is a good decision and I am pleased with it," Brentford head coach Thomas Frank said.
"I feel sorry for the Bolton fans, staff and players because they are in a mess and it is not nice to be in a situation like that.
"Bolton as a club is one of the bigger ones in England, with a massive history. I don't think any club should be in a situation like that so I hope deep down that they can turn it around and come out on the other side."
An eventful day at Bolton Wanderers
Earlier on Friday, the EFL said it was "aware" of comments made by potential owner Laurence Bassini, who has said he is in full control of Bolton Wanderers, despite the club saying the takeover was off on Thursday.
Former Watford owner Bassini's intended purchase of the Championship club was originally announced on 17 April, however the takeover is still unresolved.
A 48-hour deadline for Bassini to provide the EFL with proof of funds for the takeover passed on Thursday evening, with the club claiming they considered his approach had come to an end.