The Barcelona forward played a key role in Argentina's march to the final at the Maracana stadium in Rio, picking up four man-of-the-match awards.
He scored four goals at the tournament, but failed to pick up the one honour eluding him after Germany substitute Mario Gotze's 113th-minute goal dashed the South Americans' dream of a third title.
Germany goalkeeper Manuel Neuer kept a clean sheet in the final and he was rewarded for a number of fine performances in Brazil with the Golden Glove award for the best goalkeeper of the tournament.
Speaking in the immediate aftermath of victory Neuer said: "It is unbelievable. The team has done superbly, not only the players, but also the team behind the team. At some point we will stop celebrating, but we will always stand up again with a smile."
Colombia's young striker James Rodriguez claimed the Golden Boot for the World Cup's top scorer honours with six goals.
Despite his country going out at the quarter-final stage, the 23-year-old's haul was never matched.
Germany's Thomas Muller ended up in second place with five goals, while Messi, injured Brazil star Neymar and Netherlands striker Robin van Persie shared third spot on four.
The Young Player award went to France midfielder Paul Pogba.