Frenchman Pogba missed the draw with Swansea on Sunday through injury while Fellaini, sent off against Manchester City just three days before, was suspended but both will be part of the squad that will travel to Spain for the first leg of the Europa League semi-final.
Eric Bailly was forced off against the Swans with what appeared to be an ankle injury joining Phil Jones, Chris Smalling and Marcos Rojo on the sidelines while Luke Shaw also limped off early on.
That leaves Daley Blind as United's only fit central defender and Mourinho confirmed he may need to shuffle his pack against the Galicians.
Asked if Jones and Smalling could make it he said: "I don’t think they will. That’s my personal opinion, I don’t think they will but I know the players I choose will give everything. It doesn’t matter if I go with [Matteo] Darmian [as a] central defender or [Michael] Carrick or Axel [Tuanzebe], I trust the boys.
"They give everything, the spirit is amazing and the group is phenomenal. Fellaini and Pogba will be back for that game so there are a little bit more in terms of options so we will give everything we have."
United's run to the latter stages of both domestic cup competitions as well as the Europa League has seen United up against it with something of a fixture pile-up over the last month.
And Mourinho admitted that should United progress past Celta he may be forced into drastic action in terms of selection in the league.
"If we beat Celta, we have the final and, in this moment, it is obviously hypothetical," he added. "The Europa League final is on the Wednesday and we play against Crystal Palace on the Sunday. Before that, we play Southampton away a few days before, so we would be playing the final with disastrous consequences.
"So, again, maybe this result is also a blessing because maybe I can bring Nicky Butt and his team to play against Crystal Palace and hopefully they [Palace] don’t need the game to stay in the division because it would be very, very bad if they needed the points and we played with the Under-23s."
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