The Argentine was one of several players lauded in the annual Liga awards, with Andres Iniesta, Xabi Alonso, Sergio Ramos and Iker Casillas coming out victorious as well
The Argentina international was also named best attacker in La Liga, beating Real Madrid duo Cristiano Ronaldo and Karim Benzema to the award.
And the new father admitted it was great honour to receive the accolade.
"For those two awards I want to thank the coaches that voted me the best forward and to my colleagues who voted me the best player," Messi told reporters.
"It's a very big honour to be able to receive these awards. I won it last year too, it's a great satisfaction and an enormous joy."
Real Madrid goalkeeper Iker Casillas was voted best goalkeeper ahead of Victor Valdes and Roberto Jimenez (Zaragoza), while Sergio Ramos beat Javier Mascherano and Javi Martinez to the title of best defender.
The award of best holding midfielder went to Madrid's Xabi Alonso, with Sergio Busquets and Benat (Betis) completing the podium, while Andres Iniesta pipped Santi Cazorla and Mesut Ozil to the best attacking midfielder award.
Iniesta said: "It's something very special because one's work is noticed and valued, and it makes you very happy.
I hope that I can have this opportunity again in future, because that would mean that I have kept growing as a player and that is what I am most concerned about."
Furthermore, Pep Guardiola was elected coach of the season, Malaga's Isco talent of the year and Carles Puyol received the fair play award, with the Catalan defender, who is still recovering from a dislocated elbow, saying he was very proud to be given the recognition.
"It's an honour to receive the fair play award being a defender," the Barca skipper said.
"It's one of the things that I've always considered important, to compete strongly but always with nobility and it is what I have tried to do since I started out until now."