Germany goalkeeper Manuel Neuer, who kept a clean sheet as his side beat Argentina 1-0 in extra time to claim their fourth World Cup, was awarded the "Golden Gloves" as the tournament's top keeper.
Four-times world player of the year Messi had a quiet game by his standards on Sunday but was the driving force behind Argentina's push to their first World Cup final since 1990.
He scored four of their six goals in the group stage, set up Angel di Maria's winner in the last 16 against Switzerland and shouldered the burden of slotting home Argentina's first penalty in their shootout win over the Netherlands in the semi-finals.
Messi also won four successive man-of-the-match awards against Bosnia, Iran, Argentina and Switzerland.
A despondent Messi took little consolation in the award.
"It's a sad prize which I won, because we wanted to lift the World Cup trophy for Argentina."
While some pundits thought Messi looked jaded after the group stage and did not influence his team as much, Argentina coach Alejandro Sabella said he was a deserving winner.
"I think Lionel reached the pantheon of the greats a while back," Sabella told reporters. "Yes, I think he deserved it. He played a great World Cup to get us where he did.
"I think it's very deserved."
Germany forward Thomas Mueller was runner-up to Messi and Netherlands winger Arjen Robben was third.
Mueller also came runner-up behind Rodriquez for the Golden Boot award. The Germany forward finished with five goals, one behind the Colombian attacking midfielder.
France midfielder Paul Pogba was named young player of the tournament, while Colombia took the Fair Play award after receiving just five yellow cards in five matches in Brazil.
FIFA also praised their positive play and the behaviour of their players and officials.