Ronaldo won in 2008, while Lionel Messi has taken the award for the past four years.
Ronaldo scored all three goals in Portugal's 3-2 victory in Sweden on Tuesday to advance to the World Cup. The Real Madrid forward also scored the only goal in the first leg in Lisbon last Friday, just ahead of the midnight deadline in Europe for the original voting window.
The decision Wednesday follows angry speculation in Portugal and Madrid that FIFA has been biased toward Messi, an Argentine who plays for Barcelona.
FIFA president Sepp Blatter told an audience of students in Oxford, England, last month that he preferred Messi as a nicer, more humble personality compared to Ronaldo, who he suggested was excessively interested in his hairstyle and appearance.
Blatter then stood up to mimic Ronaldo's style on the field, which he described as like a "commander."