Messi was second in the vote and Frenchman Antoine Griezmann third.
“I’m very happy and I can say that 2016 was the best year of my career,” said Ronaldo as he was presented the award by FIFA president Gianni Infantino.
Messi missed the ceremony along with all other Barcelona players who had been invited.
“With the aim of prioritising preparations for Wednesday’s game against Athletic Club, FC Barcelona have decided that the players recognised in the awards will not be travelling to Switzerland for the ceremony,” said the club in a statement.