Colchester's goals came from Tarique Fosu-Henry, Chris Porter and Macauley Bonne, while Sandro Semedo netted for Orient, before home fans took to the pitch in the 85th minute to protest against club owner Francesco Becchetti.
After an initial announcement that the match had been abandoned, the EFL announced that they would conclude the game from the 85th minute, around two hours after the fans had been removed from the pitch.
A statement from the EFL 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 playoffs."
Orient were relegated from the Football League for the first time in their history last weekend.