The 25-year-old edged out fellow Liga star Cristiano Ronaldo, who hit the back of the net an impressive 46 times, in comparison to Messi's haul of 50.
That tally was enough to break former Dinamo Bucharest striker Dudu Georgescu's record of 47 goals, which has stood since the 1976-77 season.
''It is a prize for scoring goals, but without my team-mates I couldn't have scored them,'' he told reporters.
"I remember goals not because of their beauty, but because of their importance.
"I am happy to win my second Golden Shoe. Although individual trophies are not what I compete for, I play to win team trophies."
The Argentine then thanked his Camp Nou employers and revealed he hopes to stay at the club for the whole of his career.
"I'm grateful to Barcelona for what they've done for me. My dream is to end my career at the club, before returning to Argentina," Messi added.
His club coach Tito Vilanova also took the time to comment on his player's achievement, claiming the forward was a unique phenomenon.
"Messi Golden Shoe? I don't think we'll ever see another player like Leo. Mainly because of the way he understands the game."
|PLAYERS WHO HAVE WON TWO GOLDEN BOOTS|
|Eusebio||Benfica||1967-68 & 1972-73|
|Gerd Muller||Bayern Munich||1969-70 & 1972-73|
|Dudu Georgescu||Dinamo Bucharest||1974-75 & 1976-77|
|Fernando Gomes||Porto||1982-83 & 1984-85|
|Ally McCoist||Rangers||1991-92 & 1992-93|
|Mario Jardel||Porto & Sporting Lisbon||1998-99 & 2001-02|
|Thierry Henry||Arsenal||2003-04 & 2004-05|
|Diego Forlan||Villarreal & Atletico Madrid||2004-05 & 2008-09|
|Cristiano Ronaldo||Manchester United & Real Madrid||2007-08 & 2010-11|
|Lionel Messi||Barcelona||2009-10 & 2011-12|