Erling Haaland - Getty Images
The Norwegian put the hosts in front only five minutes into the match and bagged his 27th league goal six minutes from time.
After the early goal, Leverkusen managed to get back into the game but six minutes after the restart it was Dortmund captain Marc Reus' turn to score with a free-kick sailing in at the far post.
Lars Bender scored with an 89th-minute penalty for Leverkusen in the former Germany international's final game before retiring.
It was also a happy finale for Dortmund coach Edin Terzic, who took over midway through the season and helped them secure a Champions League spot for next season and steered them to victory in the German Cup.
Terzic is leaving to make way for Marco Rose next season.
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