It is believed Mkhitaryan will be part of a player swap that will bring Alexis Sanchez to Old Trafford during the January transfer window.
And having earlier insisted the Armenia international would be in the squad for Monday's fixture, Mourinho admitted that his decision to exclude the 28-year-old had much to do with the transfer speculation.
"I would lie if I said it was a pure tactical decision," Mourinho told Sky Sports . "It was just a choice of the players that we know, in this moment, they have 100 per cent their heads in Manchester United.
"No doubts about the future. I don't think it's easy for a player to play when there are doubts about his future. It's added pressure that a player doesn't need, so I think it's the best for him and for us, while the doubt is in the air, to protect him."
Mkhitaryan is expected to be part of the deal which will see Alexis complete a move worth around £35 million to Arsenal, with the Red Devils having usurped neighbours Manchester City with a late bid for the Chilean's signature.
United signed Mkhitaryan from Borussia Dortmund in the summer of 2016 for around £30m but has struggled to leave a lasting impression at the Theatre of Dreams, spending two lengthy periods out of the first-team picture during his 18 months in Manchester.