The 24-year-old Argentina international beat Real Madrid ace Cristiano Ronaldo, and his Barcelona team-mate Xavi Hernandez to the award which was held at the Grimaldi forum in Monaco.
It caps off a memorable season which saw him score a sublime 53 goals in all competitions to help his side enjoy a flawless campaign in La Liga and the Champions League as they won the double.
Messi also struck in last week's Supercopa as Barcelona added more silverware to their trophy room.
The Argentine declared himself delighted with the award, and gave the credit to his team mates for a stunning year in Spain.
"I am honoured to win this award and I want to thank my team-mates. We all want to win more and all the time and this is what pushes us to continue. The cohesion of the dressing room is what gives us the strength," he affirmed.
A panel of 53 sports journalists representing each of the Uefa member associations made their final decision ahead of the Champions League draw with Messi finishing ahead of Ronaldo, and Xavi.
The Argentina ace thus tops the 10-man shortlist which also included Barcelona colleagues Andres Iniesta, and Gerard Pique.
|1||Lionel Messi|| ARG
|3||Cristiano Ronaldo||POR||Real Madrid|
|4||Andres Iniesta|| SPA
|5||Radamel Falcao|| COL
||Porto/ A Madrid|
|6||Wayne Rooney|| ENG
|7||Nemanja Vidic|| SRB
|| Manchester United
|8||Zlatan Ibrahimovic|| SWE
|| AC Milan
|9||Gerard Pique|| SPA
|10||Manuel Neuer|| GER