The Armenian was overjoyed after Kevin Grosskreutz's late winner at the Stade Velodrome earned Die Schwarzgelben a place in the Champions League knockout stages
Last season's losing finalists were on the verge of elimination as they were drawing 1-1 at the Stade Velodrome, while Napoli were defeating Arsenal at the Stadio San Paolo.
However, Kevin Grosskreutz's 87th-minute winner saw Jurgen Klopp's men sensationally leapfrog both the Partenopei, who bowed out, and the Gunners to progress to the round of 16 as winners of their pool.
"It was a tough group this year and maybe there were people who doubted that we could finish top or even second this time. Perhaps we pulled off the impossible," Mkhitrayan told Uefa's official website.
"It was important to finish top because Dortmund were finalists in this competition last year. I'm very proud we got it because throughout the group stage we've had problems with red cards, injuries and so on. In spite of that, we still had players who could come in and play a great game.
"We're very proud. We played a great game and, although we didn't score all our chances, we managed to score a second goal.
"We could have ended up first or third in the group but we did our job well and took first place."
Dortmund resume their Bundesliga campaign Saturday when they travel to Hoffenheim.