The Argentine's two-goal display against Santos was enough to earn him the personal honour, as the Blaugrana celebrate the title of world champions in Japan
The 24-year-old was chosen ahead of team-mate Xavi and Peixe star Neymar, who finished second and third respectively, to receive the title after the final whistle of Sunday's match.
Messi hit twice in a 4-0 victory to confirm Barca as world champions, hitting the first and last goals of a game which the Catalans never looked like losing.
Xavi was recognised for setting up Messi for the opening goal, as well as for scoring the second for the Blaugrana midway through the first half. Neymar, meanwhile, was a key figure in Santos' semi-final victory over Kashiwa Reysol, where the Brazilians ran out 3-1 winners to set up a final clash with Barca.
Messi and Xavi's performances helped to secure a fifth title of the year for the club. Barcelona had already lifted the Champions League, Primera Division, European Super Cup and Spanish Supercopa trophies over 2011, while Neymar missed out on his own personal quadruple; having won the Paulista and Copa Libertadores with Santos, and the South American Under-20 Championship with Brazil.