The 25-year-old Messi scored a Spanish-league record 50 goals for Barcelona, edging out fellow Spanish league star Cristiano Ronaldo of Real Madrid by four goals.
Messi dedicated the award to his teammates, with Xavi Hernandez and Carles Puyol present for the ceremony in Barcelona.
"It is a prize for scoring goals, but without my teammates I couldn't have scored them," Messi said. "I share this award with them as I always do.
"I don't fight for individual awards, I fight for titles. My goals are reclaiming the league crown, winning the Copa del Rey and the winning the Champions League again. Those are my goals, team goals."
The Argentina international won his first Golden Boot in 2010 for his 34 goals that helped Barcelona win the league title.
Messi is among the favourites to win the 2012 Ballon d'Or for the world's best player.
"We won't see another player like him, and if we do, it won't be for a very long time," said Barcelona coach Tito Vilanova. "It's not just for the goals he scores, but for how he sees and understands the game, that is what makes him so great. On Saturday, he ran 50 metres to defend a corner in the 89th minute with a 5-0 lead. Not many players would have done that."
Luis Suarez Miramontes, the former Spain international and 1960 Ballon d'Or winner, presented the award.
Messi, nicknamed "The Flea" for his uncanny ability to dribble through defenders, has shattered a number of records over the past year.
He scored an unprecedented 73 goals in all competitions for Barcelona last season, breaking the previous European club record of 67 goals set by Bayern Munich's Gerd Mueller in 1972-73 and the prior world club mark of 70 established by Archie Stark of Bethlehem Steel in the American Soccer League in 1924-25.
In March, Messi passed Cesar Rodriguez's 57-year-old milestone of 232 goals to become Barcelona all-time leading scorer. He also scored a European Cup-record-tying 14 goals in the Champions League, where he netted a record five goals in one game.
Messi has scored 17 goals in all competitions to start this season, and has his sights set on yet another milestone he is sure to reach very soon. He is just two goals away from equaling Brazil great Pele's feat of 75 goals for club and country in one calendar year, set in 1958.
"Obviously, it's an honour to be close to the numbers of a person who is so important to football," Messi said. "But, again, they are only statistics.
"My goal is to win as many titles as I can before the end of my career. I have always been like that. Then I can look back at what I have won and take stock of my career."