The Argentine struck the only goal of the game as the Primera Division crown returned to Camp Nou for the first time since 2013
Barca had looked destined to bring the title back to Catalonia ever since Luis Suarez's winner against Real Madrid in March, and the Catalans did exactly what was required a year to the day after Atletico won the crown at Camp Nou.
Messi, Suarez and Neymar have led the way for Barca, scoring 79 goals between them in La Liga, and, fittingly, it was the former who sealed the title with a typically clinical finish just after the hour mark.
Suarez missed out due to a hamstring injury picked up in midweek, and Barca were less fluid than usual in attack without the Uruguayan.
But Messi's brilliance eventually shone through 25 minutes from time, as he beat Jan Oblak from inside the area after taking a sublime touch from Pedro's pass for his 54th goal in as many games this season.
Neymar should have doubled Barca's lead shortly after, but the Brazilian's wild shot from Messi's perfect throughball mattered little as Barca wrapped up their seventh title in the last decade, with Copa del Rey and Champions League finals still to come.
Atletico made it clear early on that they would not relinquish their title without a fight, enjoying a particularly bright opening 10 minutes.
But Oblak was called into action to twice deny Messi, before the Argentina captain then grazed the roof of the goal with a free-kick after Diego Godin had brought down Dani Alves.
Alves then went close himself just before the interval, though Oblak confidently turned his speculative long-range drive over.
Atletico began the second period better, and Godin went close to putting the home side ahead in the 51st minute, heading just over following a fine delivery from Koke.
Fernando Torres was the next to try his luck, and the striker forced Claudio Bravo into a crucial save at his near post.
But Barca finally broke the deadlock with 65 minutes on the clock, Messi proving decisive yet again.
The 27-year-old received a pass inside the area from Pedro, coolly dragged the ball past a defender with his first touch and duly stroked it beyond Oblak's reach through a crowd of players.
The in-form Neymar then uncharacteristically spurned a one-on-one chance that could have put the game - and title - beyond doubt.
Guilherme Siqueira's long-range effort three minutes from time had Bravo scrambling and Barca hearts in mouths, but the Catalans held on with relative comfort to earn Luis Enrique the title in his first season in charge.