Messi clinched the award – handed to the player with the most league goals in any of Europe's top-flight leagues – for the third consecutive year, beating Kylian Mbappe by three following Paris Saint-Germain's defeat Friday.
Mbappe needed to score five goals in PSG's Ligue 1 finale to collect the Golden Shoe, however, the French sensation could only manage one in a 3-1 loss at Reims.
Messi now has two more Golden Shoes than Juventus superstar Cristiano Ronaldo, who last won the award in 2014-15.
The 31-year-old Messi led Barca to back-to-back LaLiga titles ahead of Atletico Madrid and Real Madrid this season.
Messi and Barcelona will face Spanish rivals Valencia in the Copa del Rey final Saturday.