Both teams struggled for chances and momentum, but the Catalans did just enough to edge out the win despite Messi departing with an injury after all three substitutes were used.
Real Madrid's 1-1 draw with Espanyol on Saturday assured the Blaugrana of the title before a ball was kicked, and that seemed to take a lot of the sting out of the high-profile encounter, with both teams looking well off the pace.
Radamel Falcao belatedly broke the deadlock six minutes into the second half, but Barca responded, with Alexis Sanchez restoring parity in the 72nd minute. A Gabi own goal turned the score around for good with 10 minutes to go.
The win puts the Catalans on 91 points for the season, and with three wins from their remaining three games, they can equal the 100-point record set by Madrid in the 2011-12 campaign.
Atletico’s gameplan from the outset was clear – deny the Catalans time on the ball. The hosts' relentless pressing was a feature of a first half that struggled for genuinely exciting moments, with the midfield battle taking center stage.
With goalmouth action hard to come by from open play, it was no surprise to see the first chance occur through a dead-ball scenario, when Diego Godin headed narrowly off target following a corner 20 minutes in.
Moments later, Atletico went close again when Falcao teed up Adrian Lopez for a shot from the edge of the area, but the forward could not find his range and angled the wrong side of the post.
The opening half rather petered out after that, with a distinct end of season feel to proceedings as both sides lacked any sort of drive or desire to force the issue in attack.
Six minutes after the restart, the game was turned on its head. Marc Bartra, who was subbed on for the injured Dani Alves, initially surrendered possession in a dangerous area. Barca failed to clear their lines in time, and Gabi slipped in Falcao, who poked home calmly from 10 yards.
The goal perhaps came somewhat against the run of play, as Barca had began the second half brightly, and the Catalans continued to look the more superior side despite going a goal down.
Sanchez blasted about a foot too high from 25 yards out, before substitute David Villa mirrored the effort from a free-kick just in front of the Atletico penalty area. The Blaugrana were handed a blow when Lionel Messi limped off to the sidelines, with all three subs alread used.
Nevertheless, with 18 minutes remaining, the visitors found a way back into the game. Sanchez played a neat one-two with Fabregas, whose return ball was stabbed toward the corner by the Chilean, wrong-footing Thibaut Courtois en route to the back of the net.
It got even better for Barca eight minutes later, when Cristian Tello’s low center was directed toward the goal by Villa and helped into the back of the net by a looping deflection off the leg of Gabi.
What little momentum Atletico had left was completely eradicated by the unfortunate own-goal, and Barca was able to close out the game to take home the win, and keep the chase for the points record alive.