Aubameyang, Mahrez, Mane on African player shortlist
The 27-year-old French-born forward will go up against Leicester City and Algeria winger Riyad Mahrez and Liverpool and Senegal winger Sadio Mane for the prize.
Mohamed Salah of Roma and Egypt and Islam Slimani of Leicester and Algeria both failed to make the final list having made it into the final five nominees.
The winners will be unveiled at a ceremony on Thursday January 5 in Abuja, Nigeria.
Aubameyang's victory last year ended Ivory Coast midfielder Yaya Toure's run of winning the trophy in four successive years.
Mahrez stands a great chance of dethroning him, though, after enjoying a stunning 2016 in which he helped Leicester win the Premier League title and won the English Players' Player of the Year award.
Zambian midfielder Rainford Kalaba, Zimbabwean forward Khama Billiat and Ugandan goalkeeper Denis Onyango are the three contenders for the prize for best African player based on the continent.