Messi, 29, finished the Liga season as top scorer on 37 goals, giving him 74 Golden Shoe points with each goal worth two points in the table.
Real Madrid were professional, if not showstopping as they clinched a first La Liga title in five years with a comfortable 2-0 victory at Malaga.
Barcelona coach Luis Enrique bemoaned a lack of consistency earlier in the season as his side came up short in their bid to catch Real Madrid.
Real Madrid coach Zinedine Zidane said clinching the La Liga title was the "best day of my professional life."
Lionel Messi and Barcelona rallied from 2-0 down to beat Eibar but it was all for naught, as Real Madrid handled Malaga to clinch the title.
Barcelona will name its new coach on May 29, two days after the Copa del Rey final, president Josep Bartomeu confirmed on Sunday.