Orient had hoped to play the match at a later date after it was finally called less than three hours before kick-off on Tuesday following an outbreak of coronavirus cases at the east London club.
But following discussions with the EFL, the Os resigned themselves to the match that did not take place and their players were informed on Wednesday afternoon.
The Ligue 2 club were desperate to play the game which was worth £ 150,000 in Sky Sports and sponsorship revenue, but it is understood that the EFL has agreed to make up some of the shortfall following talks of ‘today.
Orient allegedly argued that the EFL was guilty of double standards after West Ham’s game against Hull on Tuesday, as Hammers boss David Moyes and two of his players returned positive tests just 70 minutes before kick off.
There is no requirement for regular coronavirus testing for EFL clubs, but Orient accepted Tottenham’s offer to pay for a series of tests after their 2-2 draw with Mansfield on Saturday, and until 17 team members returned positive results.
The club have also argued that they were being punished for accepting Tottenham’s offer when Brentford and Hull rejected opposition Premier League offers to be tested ahead of their respective third round matches.
The rules of the competition state that a club lose the game if they are unable to play due to a coronavirus outbreak, but Orient has claimed they have a team ready to play.
Spurs will progress to a fourth-round clash against Chelsea, which leads Barnsley 5-0 at Stamford Bridge.
Asked about the prospect of a reshuffle on Wednesday, Spurs manager Jose Mourinho said: “I have no idea, I was ready to play yesterday.
“I’m not happy but I’m dealing with our schedule, I’m dealing with my bad feelings about the unfair schedule we have and I was ready to play yesterday. We didn’t and now I’m ready to play again tomorrow. I do not do it. don’t know anything else.
“It was difficult because we didn’t know what to do, even on the day we had a training session I didn’t know if it was a training session with a game or a training session without match.
“It wasn’t easy but we managed to find a balance and keep the players active until the moment we weren’t going to play the game. “