The home side surged into an early 2-0 lead as they looked to end a run of three straight defeats in all competitions, with the fit-again Kylian Mbappe and Neymar getting on the scoresheet despite a bright start from Lille.
Things soon started going wrong for Christophe Galtier against the team he guided to the title in 2020-21, though, with Lille turning the game on its head to take a 3-2 advantage and PSG also losing Nuno Mendes and Neymar to injuries, the latter being stretchered off.
With pressure beginning to grow, though, Galtier's two main men stepped up to the plate as Mbappe made it 3-3 before Messi stole the headlines off his teammate with the winning free kick five minutes into stoppage time.
The result temporarily lifts PSG eight points clear at the top of the table, and perhaps more importantly ends a poor run of form which had seen them lose three times in three different competitions in the space of a week.
The home side, who had hammered Lille 7-1 in the reverse fixture between the last two champions of Ligue 1, looked as though they could threaten a repeat of that chastening scoreline when they raced into a 2-0 lead inside the opening 17 minutes.
The returning Mbappe got the first of those with a brilliant solo effort after 11 minutes, when he cut inside from the left and skipped between two defenders before steering the ball past the keeper - a move which saw Lille skipper Jose Fonte injured in the process.
Neymar joined his strike partner on the scoresheet just six minutes later when he turned the ball into an empty net after a one-two with Vitinha, who managed to smuggle the ball back to him ahead of Lucas Chevalier.
However, that two-goal advantage flattered the home side, with Lille looking an omnipresent threat - Timothy Weah threatened with an effort inside the opening minute, and Gianluigi Donnarumma was needed to deny Jonathan David headers on two occasions.
Messi had also come close at the other end before the deadlock was broken, but Lille's first of the afternoon was certainly not against the run of play when Bafode Diakite glanced a header into the corner.
There was more bad news for the champions with Nuno Mendes limping off in the first half, and Neymar's withdrawal on a stretcher added a major further blow with a Champions League second leg against Bayern Munich on the horizon.
That misery was only compounded when Lille levelled things up before the hour mark, although PSG could feel justifiably upset with the controversial decision to penalise Marco Verratti for an apparent pull in the box off the ball from a corner.
David stepped up to tuck away the spot kick, and just 11 minutes later Galtier's side found themselves staring down the barrel of a fourth successive defeat across all competitions when Jonathan Bamba was released down the right channel and hammered a powerful strike past Donnarumma at the near post.
Mbappe was visibly upset with his teammates after they fell behind, but as has so often been the case it was the Frenchman who dragged them out of the mire with his second of the game to level things up once again in the 87th minute.
Juan Bernat collected the ball from Verratti on the left flank and cut the ball back for Mbappe to fire into the bottom corner on the stretch.
Not even that brace was enough to steal the show for Mbappe, though, as Messi, who had been near-anonymous in the game up to that point, was the man to secure all three points for the hosts when he won and converted a free kick deep into stoppage time.
The Argentine lined up the central set piece from around 25 yards out with his name ringing around the Parc des Princes, and he duly curled it in off the inside of the post to cap off a thrilling contest in the French capital, and to leave Lille heartbroken as their Champions League hopes took a major hit.