The Armenia international had spent another spell on the sidelines with a hamstring injury, but started the game in Russia which went ahead despite concerns from Manchester United about the state of the pitch.
Mkhitaryan opened the scoring in the 35th minute after a cutback from Zlatan Ibrahimovic, but United were pegged back by their hosts eight minutes after the break as Aleksandr Bukharov's effort beat Sergio Romero.
