The Gabon international scored two goals in the 4-3 victory, taking his season total to 31 – one more than Bayern Munich striker Robert Lewandowski.
"The Torjagerkanone means a lot to me," Aubameyang said. "It was a great effort - made by the whole team.
"I am grateful to everybody: the training staff, my fellow players and everybody who works for the club. It is just great."
Lewandowski was followed by FC Cologne's Anthony Modeste, who netted 25 times in 2016-17, and RB Leipzig's Timo Werner, who had 21 goals.
The Poland international was denied a third "kicker Torjägerkanone" in four seasons: Lewandowski won the award in 2013-14 with 20 goals and again in 2015-16 with 30 strikes.