Shakers owner Steve Dale had been given until 5pm on Tuesday to come up with a plan for paying the club's debts and funding them going forward or sell them to someone who can.
It had been hoped that C&N Sporting Risk would be the answer but the London-based firm pulled out of the deal 90 minutes before the deadline, citing concerns over the club's confusing debt structure.
And then, just when all hope seemed lost, Dale claimed he had received three new bids for the club, prompting fans, politicians and pundits to call for more time to explore these options.
But shortly after 11pm, the league revealed its verdict.
In a statement, it said: "The EFL board met earlier this evening and, after a long and detailed discussion, determined that Bury FC's membership of the English Football League be withdrawn after the deadline passed at 5pm today (Tuesday 27 August) without a successful resolution."
Having already postponed Bury's first five scheduled league games and kicked them out of the EFL Cup, the league had made it clear to Dale there would be no more added time after he was given an extension to the last deadline on Friday night.
League One will now proceed with 23 clubs for the remainder of the season and only three clubs will be relegated in order to bring the division back to 24 teams next season. That plan, however, could change if Bolton are also expelled in the coming days.
EFL executive chair Debbie Jevans said: "Today is undoubtedly one of the darkest days in the league's recent history. The EFL has worked determinedly and tirelessly to avoid this outcome and it is with a heavy heart that this situation has been forced upon us.
"The EFL has to place the integrity of our competitions at the heart of every decision we make, and we simply cannot allow this unacceptable situation to continue or countenance the prospect of postponing further fixtures.
"I understand this will be a deeply upsetting and devastating time for Bury's players, staff, supporters and the wider community. There is no doubt today's news will be felt across the entire football family.
"No one wanted to be in this position but following repeated missed deadlines, the suspension of five league fixtures, in addition to not receiving the evidence we required in regard to financial commitments and a possible takeover not materialising; the EFL board has been forced to take the most difficult of decisions."
Bury captain Neil Danns said the club's expulsion from the English Football League had "destroyed lives".
Asked if he had a message for owner Steve Dale, Danns told talkSPORT radio: "I would say look what you've done.
"This should never have happened. If you thought you could not move this club forward in a positive way you should never have taken over because you've literally destroyed lives, because that's what this football club meant to so many fans."
He added that "serious questions have got to be asked" about what had happened.
"When you see the devastation of the fans I just think I have to say something," he said. "It's unbelievable. I still can't believe it."
Dave Giffard, chair of Forever Bury Supporters Club, told BBC Breakfast that the fans are discussing their next move.
"We have got a meeting this morning to look at our next move. What we would like to do is try and save this football club," he said.
"If we have to restart as a phoenix club we would like to get hold of this ground. We have the support of the council."