The Armenian engaged in a fascinating battle with Schafer, who looked in inspired form as he kept Dortmund at bay in the opening half on Saturday.
But the floodgates opened early in the second half, as Mats Hummels' scrappy strike was followed by a Robert Lewandowski effort from 20 yards.
Mkhitaryan finally got the goal he so craved in the closing stages, but was quick to hail Schafer's display afterwards.
"Schafer was great, but I did not give up and always believed in my goal," he told the club's official website. "In the end it worked out and... I am very happy."
"Today, we have done everything to get the three points," he continued. "The match against Hamburg was not in our minds, rather have the good game against Zenit (4-2 UEFA Champions League victory) during the week.
"For us always, we always count only the last and the next game. At the end we won today and it was very deserved."
"We need to win as many as possible to keep the second place," he added. "The season is still long, it will be a hard road."
