The Armenian playmaker has sat out seven of the Red Devils' matches over the last month, failing to even make the bench after slipping well down the pecking order.
Mkhitaryan was accused of "disappearing" in big games by Mourinho in the early stages of the season, despite United flying high at the time, and the Portuguese is not prepared to sacrifice squad balance for the sake of his £26m signing.
"I can only have six [outfield] players on the bench and I try to have some balance on the bench," he told reporters. "I had two defenders and [Daley] Blind who can play in different areas.
"I had Ashley Young to cover me all the wings and the wing-back position. I had [Ander] Herrera as a midfield player, Zlatan [Ibrahimovic] as a striker and Marcus [Rashford] as a second striker and winger.
"I played [Anthony] Martial, [Juan] Mata and [Jesse] Lingard in the team. To have Mkhi means that I don't have one of them and, in this moment, I believe the other ones they deserve [the chance to play]."
Mkhitaryan registered five assists and a goal in his first five Premier League outings this season.