Dortmund took over the reins from kick-off and needed only 16 minutes to work out their first chance through Aubameyang, who headed a promising opportunity over the bar here on Saturday, reports Xinhua.
The Gabon international scored moments later as he nodded home Andre Schuerrle's cross to the far post in the 17th minute.
Mainz responded well but neither Christian Clemens nor Karim Onisiwo were able to restore parity before the break.
As the match progressed, Dortmund gained control yet the hosts missed few shots on target before a penalty allowed Aubameyang to seal his brace, and to put the game beyond doubt in the 89th minute.
Mainz did not give up and were able to reward their efforts as Yoshinori Muto reduced the arrears in the closing period.
Monchengladbach and Leverkusen staged a fast paced encounter with many chances at both ends of the pitch.
Monchengladbach's Andre Hahn opened the scoring, beating onrushing goalkeeper Bernd Leno just at the stroke of halftime.
Leverkusen tried to respond after the interval and their efforts paid out in the 80th minute after substitute Joel Pohjanpalo headed home for the equaliser.
Monchengladbach remained unimpressed and responded just five minutes later as Lars Stindl grabbed the 2-1 winner, thanks to a through ball from substitute Thorgan Hazard.
Elsewhere, Schalke suffered a 0-1 defeat against ten-man Frankfurt due to a first-half goal from Alexander Meier.
Cologne moved 2-0 past Darmstadt as Anthony Modeste and Marcel Risse scored.
Hosts Hamburg were held to a 1-1 draw by Ingolstadt.
Wolfsburg reaped three points at Augsburg after Daniel Didavi and Ricardo Rodriguez netted in a 2-0 away victory.