Although available, forward Martial, having started the previous game, was not part of the United 18 for Thursday's 4-0 Europa League win over Feyenoord.
Martial scored 17 goals in his first season with United last term, but has netted only twice so far in 2016-17.
When asked about the 20-year-old Frenchman's omission, Mourinho confirmed Martial had not been injured, he said: "He was okay for the game, it was just an option.
"He played on Saturday (in the 1-1 draw against Arsenal) and I cannot play with 12 players. I cannot have, (with those) on the bench, 19 or 20.
"You wanted to see Mkhitaryan (who shone on what was only his second United start) and I wanted to too. I cannot play all of them at the same time.
"Anthony played against Arsenal, and (Thursday) was the moment to give a chance to Mkhitaryan to start.
"So it was just an option - and I think the players, they have to win their positions.
"They are friends, they are colleagues, they work together every day, but in the end they compete between themselves to have more chances to play."