Mkhitaryan was a regular starter for the first few months of the season, finding the net during the 4-0 win over Everton and the 4-1 Champions League victory at CSKA Moscow.
However, the Armenian was left out of the matchday squads for last weekend's 4-1 Premier League victory over Newcastle United and also sat out of Wednesday's 1-0 Champions League defeat against Basel.
Asked why Mkhitaryan was omitted, Mourinho told reporters on Friday: "I was not happy with his last performances and I am not speaking about one or two. I am speaking about three, four or five. He started the season very well and, after that, step by step, he was disappearing.
"His performance levels in terms of goal scoring, assists, high pressing, recovering the ball high on the pitch, bringing the team with him as a number 10, were decreasing step by step. That was enough because the others, they work to have a chance, everybody works to have a chance. So, it is as simple as that."
Mkhitaryan, who joined United from Borussia Dortmund in 2016, made a modest start to his Red Devils career and did not start a Premier League game in almost three months after being substituted at half time in the defeat to Manchester City last September.