Christophe Galtier's men travelled to the Stade de la Meinau knowing that a point would be enough to confirm a first-placed finish in the French top flight with a game to spare.
PSG held a six-point lead over Lens before kickoff on Saturday evening, and with no Neymar or Hugo Ekitike available, Messi and Kylian Mbappe joined forces at the tip of the attack.
The champions struggled to string successful attacking sequences together in the first half, but on the stroke of the hour mark, Mbappe and Messi combined for the latter to break the deadlock.
Having shown excellent control to bring down Danilo Pereira's long pass on the left-hand side, Mbappe waited for Messi to make his run into the box before setting up the Argentine to fire home into the far corner.
PSG were unable to hold on for the win as former Parisiens forward Kevin Gameiro levelled for the hosts late on, but Galtier's side still obtained the point required to wrap up an 11th Ligue 1 crown.
Another slice of personal history was written for Messi as well, as his opener at the Stade de la Meinau marked his 496th goal across the big five European leagues.
The seven-time Ballon d'Or winner found the back of the net 474 times in La Liga with Barcelona, and he now has 22 Ligue 1 goals to his name since arriving in Paris in 2021.
Messi had drawn level with Cristiano Ronaldo on 495 strikes during April's 3-1 win over Lens, but he is now the outright record-holder after ending a four-game streak without scoring in Ligue 1.
The 35-year-old now possesses a total of 32 goals and 35 assists from 74 matches in a PSG shirt, scoring 21 goals and setting up 20 more in 40 outings across all tournaments this term.
Sixteen of Messi's goals in 2022-23 have come in Ligue 1, where he has also set up a division-high 16 goals, five more than teammate and closest challenger Neymar.
However, the former Barcelona man has likely played his penultimate game for PSG, as he is expected to leave when his contract expires at the end of the season.
The relationship between Messi and the club became strained when the attacker took an unauthorised commercial trip to Saudi Arabia at the beginning of May, leading to a fine and initial two-week suspension being imposed upon his return.
PSG rescinded Messi's ban after he posted a public apology, but the French champions seemingly have no desire to activate the 12-month extension option in his contract amid persistent talk of a Barcelona homecoming.
Messi is set to make his farewell appearance at the Parc des Princes when PSG host Clermont in their final Ligue 1 game of the season next Saturday.