Ronaldo has now won the award four times (2008, 2013, 2014 and 2016) but still haven't rivalled Messi's winning streak of 5 Ballon d'Or titles in total.
"It is a special moment. It means that all my sacrifice was worth it. I feel very happy to win this. I worked very hard.
"A lot of people helped me get here, and it is not easy to get here. You can count on one hand players who maintain this level year after year. I am one of them, and that is a source of pride for me."
In 2016, Ronaldo helped his team Real Madrid win the Champions League and captained Portugal to an Euro trophy win - the country's first major title since the beginning of time.
The award gala night for the 2016 Ballon d'Or - where prizes and silverware will be handed to winners - will hold on January 9, 2017.