Ernesto Valverde's men went into the game knowing that only a victory would allow them to wrap up the title this weekend.
Atletico Madrid had kept the heat up on the Blaugrana with their own defeat of Valladolid, to move within six points of the leaders prior to kick-off.
But Barca made no mistake as Messi's goal proved the difference at Camp Nou and confirmed a second successive Liga title.
The Argentine netted after 61 minutes in Saturday's clash to finally break the Valencians' resolve, having been denied on multiple occasions by goalkeeper Aitor Fernandez.
Now nine points clear of Atletico with three games left to play, Barca's superior head-to-head record means that the Colchoneros' slim chances of wresting the title away have now been extinguished.
The newly crowned champions have lost just two games so far domestically, to Leganes and Betis, scoring 86 goals and conceding 32.
Messi in turn took his personal tally for the 2018-19 league season to 34 goals, 13 clear of nearest Pichichi challengers Karim Benzema and Luis Suarez.
La Liga represents the first step in a possible third treble for Barcelona, who capitalised on a disappointing season for rivals Real Madrid to lead the race from start to finish this term.
The Catalans also remain active in the Copa del Rey, where they will dispute the final against Valencia on May 25; and the Champions League, which will resume with Barca's semi-final first leg clash with Liverpool on Wednesday at Camp Nou.
This latest title also underlines Barca's recent dominance of the Primera Division.
The team has finished top of the pile in eight of the last 11 Liga seasons dating back to the start of Pep Guardiola's reign, with only Real and Atletico able to break their monopoly over that period.
The Blancos came out on top in 2011-12 and 2016-17, while Atletico narrowly defeated Gerardo Martino's Barca side to the title in 2013-14 in a thrilling last-day conclusion to the race.