The 26-year-old Messi helped Barcelona win the 2012-13 Spanish league by scoring 46 goals despite missing several games with a right hamstring pull near the end of the season.
Messi also won the award for 34 goals in 2009-10, and a Spanish record 50 in 2011-12.
The first player to receive the award three times, Messi dedicated his latest trophy to his family and his teammates, calling it a team award.
"This is a beautiful award that goes to the entire squad for what it has done," Messi said. "It is a group award more than an individual one because those are a lot of goals. I wouldn't have won it without them, this one or the previous ones."
Messi is recovering from a left hamstring tear that will probably keep him sidelined for the rest of 2013. It was his third leg injury of the season. Before his latest injury, he had eight goals in 11 league appearances.
After receiving the trophy from former Barcelona star Hristo Stoichkov, Messi said his leg was feeling better while remaining cautious about rushing back.
Several teammates, including Cesc Fabregas, Xavi Hernandez and Carles Puyol, along with club president Sandro Rosell were in attendance.
Messi has won the world player of the year award an unprecedented four years in a row. He is again nominated this year, but he has tough competition from Real Madrid rival Cristiano Ronaldo and Bayern Munich star Franck Ribery.
Messi has played a major part in Barcelona's impressive run of titles over the past decade. He has won three Champions Leagues, six Spanish leagues, two Copas del Rey, two Club World Cups, six Spanish Super Cups and two European Super Cups.
Barcelona's all-time leading scorer, Messi's 65 goals in the Champions League is second to former Madrid striker Raul Gonzalez's 71.