The Armenian striker opened the scoring at the Allianz Arena on 20 minutes, with Marco Reus and Jonas Hofmann adding to the tally as the club earned a 3-0 win against the newly-crowned champion.
Die Schwarzgelben have tightened their grip on the Bundesliga runner-up position, extending the lead over Schalke to three points, and Mkhitaryan hailed the positive impact the result could have after losing to Real Madrid in the Champions League quarterfinals.
"We are very, very happy because it was a very difficult match and we have defended second place against Schalke," the 25-year-old was quoted in Der Western. "It's hard to describe how happy I am to have made the 1-0. It was very important that we defended well, scored the first goal and then in the second half could concentrate on the counterattack.
"After the match against Real Madrid, I was annoyed about the missed chances. But that's football - it just goes on. And now our heads are up again."
The Armenian's sentiment was echoed by fellow goalscorer Marco Reus, believing that BVB has done itself credit after the disappointment of being knocked out of the Champions League.
"We could only play the way we did today," the German winger said.
"We have done very well especially in the first half and took our chances very well. For us it was important that we attacked early and took the ball far forward. Then it's not so far in front of goal, which was, I think, today the key to success. This week has brought us absolutely to the front."
Dortmund is second in Bundesliga with 61 points from 30 games, three ahead of Schalke.