Mkhitaryan started in United's Europa League second leg clash away to Saint-Etienne on Wednesday, opening the scoring after just 16 minutes. Nine minutes later however the Armenia international left the pitch clutching his hamstring to be replaced by Marcus Rashford.
Mourinho told reporters after the win in France he felt the former Borussia Dortmund star had "no chance" of featuring on Sunday, also fearing Michael Carrick would not recover in time after the midfielder appeared to pick up a calf problem.
The United boss struck a much more optimistic note over Carrick when addressing the media on Friday however, also revealing Phil Jones is in contention to return from a foot injury.
"Michael [Carrick] is available," Mourinho said. "Clever, experienced. He left the pitch [against Saint-Etienne] in the right moment so Michael is available. Mkhitaryan is out and Jones, let's see and decide tomorrow."
Rooney, who confirmed on Thursday he will not be leaving the club amid rumours of a move to the Chinese Super League, returned to training this week after a minor injury. Mourinho suggested his skipper is unlikely to start on Sunday but says he will have some role to play.
"Wayne's fine, he's training with the team. He was not selected for Saint-Etienne because he was not ready to play but he was ready to have one more important training session and no doubts, no doubts, he is involved in the game."
United opted against major changes for their midweek game in France but Ander Herrera was one notable absentee as he served a one-match suspension. He is expected to return to the starting XI at Wembley.