The Gabon captain finished just 0.2% ahead of Bayern Munich’s Robert Lewandowski, who was the top scorer in the league last season.
The award is voted for by the German players’ union, the VDV.
“It’s a great honour to be recognised and appreciated by your fellow colleagues,” Aubameyang said.
“This is for everyone at Dortmund and our amazing fans.”
Aubameyang, who is also the African Footballer of the Year, scored 25 goals and made six assists in 31 league games as Dortmund finished runners-up in the Bundesliga.
He also scored 39 goals in all competitions last season and becomes the first African to win the VDV award since its inception in 1998.
He is also the only African named in the Bundesliga team of the year.
Aubameyang and Henrikh Mkhitaryan are joined in the ‘Team of the Season’ by team-mate Mats Hummels, who will join Bayern Munich this summer.