After being the runners-up in the final for the past three years, the Black and Yellows really wanted to win this time round and they got off to a perfect start when a brilliantly taken goal from Ousmane Dembélé gave them the lead in the eighth minute.
The Eagles though showed why they had made it through to the final when they equalised just before the half hour mark when Ante Rebić finished off a fine move.
Dortmund though regained their lead in the second half when Aubameyang scored penalty which saw Thomas Tuchel's side finally get the trophy that had eluded them for the past few years.
Dembele's stunning strike gave Dortmund the perfect start
Unsuprisingly, Dortmund made a strong start to the game and that led to them taking the lead when a great passing move ended with Dembélé scoring a stunning goal.
Łukasz Piszczek recieved the ball and played it too Dembele, who twisted and turned inside the box while beating two defenders, and rifled a left-footed shot into the top corner of the net.
Marco Reus almost made it two soon after when he volleyed a corner towards goal but Lukas Hradecky got down well to make a smart save.
The Eagles dominated the second part of the first half as Rebic levelled proceedings
It turned out to be the turning point in the half for Frankfurt as from their they started to dominate the ball and they should have levelled when a great cross from Rebic found Timothy Chandler unmarked in the box but he put his header over the bar.
It didn't matter though as only a few minutes later, the Eagles did get an equaliser when a fantastic pass from Mijat Gaćinović found Rebic in the box and he confidently put the ball into the net past a helpless Roman Burki in goal.
Dortmund at this stage were all over the place and they were lucky to not fall behind when Haris Seferović saw his left-footed curling shot from the edge of the box come back off the post.
The Eagles continued to dominate the ball for the rest of the half but didn't create any other chances as they would have went in at the break feeling that if the pattern of the game stayed the same, they had a great chance of winning the match, while Dortmund needed to regroup and play better.
Tuchel's half-time team talk had an effect as Dortmund started the second half strong
It was clear from the start of the second half that Tuchel had some choice words for his players as they started strong and almost retook the lead when Shinji Kagawa's cross-shot was cleared off the line.
Minutes later, they had another shot cleared off the line when Aubameyang's overhead kick was heading into the net but Marco Fabian turned the ball onto the bar.
The Eagles just couldn't get going at all in the second half and they fell behind for the second time when Christian Pulisic, on as a second half substitute, was fouled in the box by Hradecky and the referee pointed straight to the spot.
Aubameyang's brilliantly taken penalty earned his side the trophy in what could be his last game for the club
Aubameyang stepped up to take it and he chipped the ball into the middle of the net with Hradecky diving the wrong way to give his side the lead in the game for the second time.
The striker could have added a third before the end of the game but his goalbound shot hit the post and went wide.
The miss didn't matter though as the Black and Yellows saw the game out with ease to finally end their run of final losses to give Tuchel and Aubameyang, who are reported to leaving the club, the perfect send off, while the Eagles should be proud of how the perfromed during the game but they fell just short.