Neymar, who has joined Barcelona from Santos for 57 million euros won the Golden Ball, awarded to the best player in the competition after a vote among the media.
Andres Iniesta of Spain and Paulinho from Brazil were second and third respectively.
The 21-year-old Neymar, who scored four goals during the tournament, said he would have the surgery on Friday before he goes to Spain.
"It's a problem that I have, my throat always bothers me, so we're going to operate to resolve it once and for all," he said in adding that it was not a serious issue.
He also urged a word of caution to his compatriots among the celebrations following Brazil's demolition of the world and European champions at the Maracana.
"Lets keep calm, let's keep our feet on the ground," he said as Brazil emerged as serious contenders to win the World Cup on home soil in a year's time. "We did very well and we are on the right track.
"We needed this time to train, we get to know each other and to work together and we are much better than we were. We won the title and that was a great end to a great tournament."
Neymar began the tournament with a brilliant strike against Japan, added goals against Mexico and Italy then ended it with another superb goal against Spain when he lashed the ball past keeper Iker Casillas just before halftime.
Spain's Fernando Torres, who scored five goals and was joint top scorer along with Fred of Brazil, won the Golden Boot for having an assist in his four matches, while Fred had one assist but played one more match.
Brazil's Julio Cesar collected the Golden Glove for the best goalkeeper while Spain took the FIFA Fair Play Trophy.
