The Barcelona star scooped the prize ahead of Virgil van Dijk, Cristiano Ronaldo and Sadio Mane, who finished in fourth place.
Messi becomes the first player in history to lift the trophy six times following victories in 2009, 2010, 2011, 2012 and 2015.
Liverpool forward Mohamed Salah finished fifth, followed by PSG’s Kylian Mbappe, while Salah’s team-mate Alisson Becker was in seventh.
However, the Brazilian did pick up an award, beating Manchester City rival Ederson to the Yachine Trophy for the best keeper.
City duo Bernardo Silva and Riyad Mahrez finished in ninth and 10th place respectively, hot on the heels of Bayern Munich’s Robert Lewandowski.
France Football had earlier confirmed released positions 11-30, which meant Van Dijk was guaranteed a place in the top 10 along with Reds team-mates Mane, goalkeeper Alisson and Egyptian superstar Salah.
The other six confirmed in the top 10 were Messi, Lewandowski, City’s Mahrez and Silva, PSG forward Mbappe and Juventus sensation Ronaldo .
The first of seven Liverpool players to have their position confirmed was Georginio Wijnaldum, the Champions League semi-final hero who shared 26th place with Real Madrid striker Karim Benzema.
Wijnaldum’s Reds team-mates Trent Alexander-Arnold and Roberto Firmino were 19th and 17th respectively, with four of the Champions League-winning team sitting in the top 10.
Aubameyang was able to claim bragging rights over his fierce north London rivals, as he finished ahead of Tottenham pair Hugo Lloris and Son Heung-min.
Meanwhile, Juventus defender Matthijs De Ligt won the Kopa Trophy ahead of Jadon Sancho and Joao Felix.
The full 2019 Ballon d’Or rankings
28= Joao Felix (Atletico Madrid)
28= Marquinhos (Paris Saint-Germain)
28= Donny van de Beek (Ajax)
26= Karim Benzema (Real Madrid)
26= Georginio Wijnaldum ( Liverpool )
24= Kalidou Koulibaly (Napoli)
24= Marc-Andre Ter Stegen ( Barcelona )
23= Hugo Lloris (Tottenham)
22= Son Heung-min (Tottenham)
20= Pierre-Emerick Aubameyang (Arsenal)
20= Dusan Tadic (Ajax)
19= Trent Alexander-Arnold (Liverpool)
18= Antoine Griezmann (Barcelona)
17= Roberto Firmino (Liverpool
16= Sergio Aguero ( Manchester City )
15= Matthijs de Ligt ( Juventus )
14= Kevin De Bruyne (Manchester City)
13= Eden Hazard (Real Madrid)
12= Raheem Sterling (Manchester City)
11= Frenkie De Jong (Barcelona)
10= Riyad Mahrez (Manchester City)
9= Bernardo Silva (Manchester City)
8= Robert Lewandowski (Bayern Munich)
7= Alisson Becker (Liverpool)
6= Kylian Mbappe (PSG)
5= Mohamed Salah (Liverpool)
4= Sadio Mane (Liverpool)
3= Cristiano Ronaldo (Juventus)
2= Virgil van Dijk (Liverpool)
1= Lionel Messi (Barcelona)