Lewandowski finished off a quick counter-attack late on to take the points, and Mkhitaryan said that the Pole was the best player on the pitch.
"[Putting away chances is] what decides these sorts of games," he told Bundesliga.com.
"Sometimes there are just one or two moments like that and you have to be there to make use of your opponents' mistakes. That's football. [Lewandowski] is simply magnificent.
"He was the best against Arsenal. How he ran, fought and coolly finished for 2-1 was indescribable. For me, he is one of the best strikers in the world."
The result leaves Dortmund, Arsenal and Napoli all on six points in the group.