Messi finished ahead of club team-mate Xavi Hernandez and Real Madrid's Cristiano Ronaldo in a poll of sports journalists who represent each of the UEFA member associations.
Messi, who scored 53 goals last season, was presented the prize on Thursday night at the UEFA Champions League group stage draw in Monaco.
"I'd like to thank all the people that voted for me, and all my team-mates," Messi told UEFA.com
"I keep all these awards at home and I still have some space for more. It's an honour to be so successful and to come up with the goods at the right time; thanks to my team-mates for helping me achieve this.
"[My motivation] comes from being at a club that's so successful and having a structure that allows us to be so successful; that was taught to me when I moved over and I've tried my best to keep it up."
Messi netted 12 times in the UEFA Champions League last season to lead Barcelona to their third European title in six years.
The award replaces the old UEFA Club Footballer of the Year award.
How they stand
1 Lionel Messi - Barcelona (39 votes)
2 Xavi Hernandez - Barcelona (11 votes)
3 Cristiano Ronaldo - Real Madrid (3 votes)
4 Andres Iniesta - Barcelona
5 Falcao - Porto (now at Atletico Madrid)
6 Wayne Rooney - Manchester United
7 Nemanja Vidic - Manchester United
8 Zlatan Ibrahimovic - AC Milan
- Gerard Pique - Barcelona
10 Manuel Neuer - Schalke (now at Bayern Munich)