Barca were confirmed as champions on Saturday night when Real Madrid could only draw at Espanyol but initially looked set to mark the occasion with defeat as they trailed to Radamel Falcao's opener when Messi limped off on 67 minutes.
But by the time their talisman had reappeared, changed and showered, on the touchline Barca had snatched away victory.
Alexis Sanchez equalised on 72 minutes, following a one-two with Cesc Fabregas, before Gabi awkwardly turned a David Villa shot into his own net nine minutes from the end.
The final whistle drew some half-hearted title celebrations from the Barca players in front of the travelling support at the Vicente Calderon.
The away fans had, however, not been treated to the most vintage of performances with both teams having reason to have their thoughts elsewhere.
Atletico will meet city rivals Real in the Copa del Rey final on Friday night, which prompted boss Diego Simeone to withdraw Falcao and Arda Turan, before Barca's decisive double.
Falcao had given his side a 51st-minute lead following an opening 45 minutes which provided few highlights.
Messi spent a large part of it riding the challenges of the Atletico defenders but it was team-mate Cristian Tello who came closest to the opener when he curled a shot wide in injury-time.
A tame match was finally given life thanks to Falcao's 34th goal of the season shortly after the re-start.
Gabi was floored by a fair challenge by Gerard Pique on the edge of the area but still had enough composure to lay the ball off to the unmarked Falcao, who toe-poked the his shot beyond Jose Pinto.
The hosts should have had a second soon after when Falcao squared the ball back for Turan but he lost the ball under his feet with only Pinto to beat.
Hopes of a second goal seemingly faded as Turan and Falcao were then subbed either side of Messi's exit but Barca broke through thanks to a slick move.
Alexis played a tight one-two with Fabregas inside the area before mirroring Falcao's poked shot to score.
Gabi was then left red-faced for the winner. Villa latched onto a pull back 12 yards out and while he scuffed his shot off target the defender conspired to loop the ball over his goalkeeper and into the net via his thigh.