Already relegated 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."