Leyton Orient’s match with Colchester United was postponed for nearly two hours after fans occupied the pitch.
Colchester eventually won the match 3-1 after home fans protesting against Orient owner Francesco Becchetti got onto the pitch in the 85th minute.
Following the lengthy postponement, players returned and played the final eight minutes behind closed doors.
A Football League statement said the game was concluded “to maintain the integrity of the competition”.
It read: “The decision to play the match to a conclusion was agreed with both managers and with the support of the match officials.
“The police and stadium security staff were happy for the match to restart and this took place at approximately 6.40pm.
“Despite requests for the fans to clear the pitch, there wasn’t sufficient movement to allow the game to restart following a pitch invasion.
“A decision was taken with the police to announce that the game had been abandoned, as it was felt this would help clear the pitch, which proved correct.
“However, it was deemed appropriate that the game needed to be played to a conclusion in order to maintain the integrity of the competition and in respect of Colchester United’s position of being able to qualify for the League Two play-offs.”
Bottom side Orient were relegated from the English Football League for the first time in their history last weekend.
Before kick-off, troubled club Orient released a statement saying that they had cleared their debts to Her Majesty’s Revenue and Customs.
However, BBC London understands some freelance contractors at the club are yet to be paid.
Colchester’s goals came from Tarique Fosu-Henry, Chris Porter and Macauley Bonne, while Sandro Semedo netted for Orient.
The win moved Colchester up to 10th place, a point adrift of the play-off places with one match remaining.
Leyton Orient manager Omer Riza told BBC Radio London:
“When I spoke to John McGreal we said we’d play normally (following the delay) but I think the players – maybe it was hard for them to warm up and get back into the speed of the game – decided to see it out for five minutes.
“I think it’s right (that the game was completed). Those are the rules we have to abide by – if we didn’t finish it now then we’d have to come back next week and that wouldn’t have been good for Colchester, the players or us.
“It was the right thing to clear the pitch, wait however long it needed and get it finished.”
Colchester head coach John McGreal told BBC Essex:
“We knew during the week something could happen in terms of fan protests.
“It was an ongoing situation once we came off the pitch. We consulted with the EFL and Leyton Orient and agreed we’d get it finished. Omer [Riza] and myself came together and didn’t want to have to come back in the week to finish it.
“The Orient fans were fine throughout. There was never any feeling of the players being in danger at all and I have to commend our supporters for their behaviour and I hope they can now look forward to next week with so much to play for.”