Bury will not be re-admitted into the Football League, the former League One side were expelled last month when a late takeover bid failed.
A meeting of all 71 league clubs decided against letting Bury return to "maintain fairness".
“While we are saddened that Bury FC is no longer part of the EFL, the Board’s difficult decision to withdraw membership was only taken after every opportunity to find a resolution was exhausted," the EFL's Executive Chair Debbie Jevans said after the meeting.
"Since then, in recognition of the efforts made on behalf of the Club, the EFL has engaged with supporters’ groups, shared their submissions with our members and debated at length the issues raised".
As a result, they also agreed only one team will be relegated from League 2 this season.
“Following the discussion today, Clubs have established that the preferred direction of travel is to reduce relegation from League Two as a means of returning to 72 Clubs. The Clubs felt that, in a difficult situation, this approach maintains fairness for all members and upholds the principle of the football pyramid.”
Clubs have also given their backing to the proposed appointment of Rick Parry as EFL Chairman.
Bury meanwhile are facing the threat of being liquidated after they served with a winding up order by the HMRC for non-paying of national insurance, with the case to be heard in the high court in London on October 16.
