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 on Tuesday night, 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and, after a long and detailed discussion, determined that Bury FC's membership of the English Football League be withdrawn after the deadline passed at 5pm today (Tuesday 27 August) without a successful resolution."
League One will now comprise 23 clubs with three relegation places, instead of the usual four.
Doncaster Rovers had been scheduled to travel to Bury this weekend.
Meanwhile, Bolton Wanderers will be kicked out of the EFL if they fail to complete a takeover in the next 14 days.
Optimism had been growing on Tuesday that Bolton would meet the 5pm deadline set by the league to announce that the deal had been approved.
But in a statement released at 11.05pm, the EFL said: "Despite further exchanges with the administrators over the course of the Bank Holiday weekend, and right up until today's deadline of 5pm, a resolution to ongoing impasse in negotiations regarding a completion of sale at Bolton Wanderers has not yet been found.
"The EFL board has therefore taken the decision to lift the suspension on the notice of withdrawal, which was issued as per the EFL's insolvency policy when the club entered administration in May 2019.
"As per the league's articles of association, this will now give the club 14 days (11.59pm on 12 September, 2019) to meet all outstanding requirements of the league's insolvency policy or its membership in the EFL will be withdrawn."