But Modric's impact in Croatia's run to the World Cup final, coupled with Madrid winning the Champions League for the third year in a row, saw him triumph. Both enjoyed bumper domestic seasons in La Liga, with Ronaldo plundering 44 goals in all competitions to Messi's 44.
Neymar finished 12th, his first time out of the top-10 since 2012.
"It surprises me as much as anyone else", he said.
"It is, at the very least, a little odd".
Among all the awards the victor of the women's Ballon d'Or was also announced, and Ada Hegerberg took the accolade after her performances for Lyon and Norway saw the former clinch the Champions League title.
The 33-year-old has already lost two major awards to his former teammate Luka Modric earlier this year.
Ronaldo's Ballon d'Or wins: 5.
And his second goal put him ahead of Arsenal legend Thierry Henry into sixth place in the all-time standings - with the Monaco manager's week getting worse when his side lost 2-0 to Atletico Madrid the following day.
Kaka was the last player other than Messi or Ronaldo to win the Ballon d'Or, the Brazilian claiming the title in 2007 while starring for AC Milan.
The ceremony will begin from the Grand Palais in Paris on Monday evening.