Spurs had been due to play Leyton Orient in round three of the competition; however, a COVID-19 outbreak in the League Two club's ranks meant Wednesday's (AEST) game could not go ahead this week.
The EFL did not make an immediate decision on the fate of that tie, but has since announced Tottenham will be given a walkover.
It means Mourinho's Spurs will host Chelsea next Wednesday (AEST), with a quarter-final place at stake.
An EFL statement read: "The round three tie scheduled for Tuesday 22 September [Wednesday 23 September AEST] between Leyton Orient and Tottenham Hotspur could not take place following the issue by Waltham Forest Borough Council of an order preventing the match being played as planned. This followed a number of Leyton Orient players testing positive for COVID-19."
Citing rule 5.1 of the competition's regulations, which is specific to the non-fulfilment of fixtures, the EFL board ruled that Orient would be eliminated.
"The club was unable to fulfil its obligations to complete the fixture by virtue of the council’s order and shall therefore forfeit the tie," the EFL statement read.