Toure had won the award for four straight years before ending up behind Aubameyan on Thursday in Abuja.
Ghana and Swansea City Star, Andre Ayew was the second runner up.
Aubameyang has been in phenomenal form for Dortmund this season, scoring 27 goals in all competitions in as many appearances.
Born in 1989, he started his career at Milan before joining Saint Ettienne in 2011 after four loan spells with clubs in France.
The 26-year-old joined Dortmund in 2013 and has since made a mark on the German club, winning two DFL Supercup in 2013 and 2014.
Although Dortmund has no desire to sell the player, several top clubs are interested in signing him with reports emerging on Thursday that Arsenal may bid for him.
With a transfer fee expected to be as high as £60m, long-term admirer Arsene Wenger may opt to look elsewhere for talent.