Messi charged from midfield toward the penalty area in the 74th minute, opening up more space as Achraf Hakimi made a dummy run to his right, and received a clever flick from Kylian Mbappe before curling a fine strike into the top right corner with the most famed left foot in world football.
"I'm very happy to have scored. I've not been playing much recently and I'm adapting to my teammates little by little," Messi said through a translator. "The more we play together the better it will become. We need to grow together and increase our level."
PSG manager Mauricio Pochettino said Messi's goal was spectacular enough to garner a rare mid-game reaction from him.
"I'm so happy to see his first goal here. He's top class. Oh I celebrated today. I don't usually celebrate goals, it's internalised. Today, I let out a shout," Pochettino said.
"I've spent long enough seeing so many Messi goals against me," the ex-Tottenham Hotspur and Espanyol manager added. "I had to celebrate the one that was for me!"
Messi netted an astounding 672 goals for Barcelona but it was his first for PSG in three starts and four games overall since a shock summer move from the Spanish club.
Under Pep Guardiola, who is now the manager at Manchester City, the pair won the Champions League in 2009 and 2011 for Barcelona, with six-time Ballon d'Or winner Messi scoring in both finals.
City had not lost its five previous meetings with PSG, winning 2-1 in Paris and 2-0 at home in last season's semifinals before losing to Chelsea in the final.
PSG started its dream attack of Messi, Neymar and Mbappe, but it was unheralded midfielder Idrissa Gueye who opened the scoring in the eighth minute. He thumped the ball into the top corner after Neymar's scuffed shot fell to him just inside the penalty area following Mbappe's cross from the right.
City should have equalised in the 26th, but instead produced a contender for miss of the season. Raheem Sterling's header from Kevin De Bruyne's cross hit the crossbar and the ball fell to winger Bernardo Silva less than two metres out.
But Silva somehow scooped the ball onto the bar with goalkeeper Gianluigi Donnarumma beaten. Donnarumma and opposite number Ederson then made a smart save each in an even first half that De Bruyne was perhaps lucky to finish, receiving only a yellow card for a dangerous tackle on Gueye's shin.
Sterling dragged a shot wide early in the second half as City caught PSG's defense asleep down the left. Donnarumma then kicked away De Bruyne's shot in the 54th as City exposed poor defending on the other flank as the Premier League champion took control.
PSG's glittering attack looked flat, as it did in a 1-1 draw against Club Brugge. Neymar shot into the side netting midway through the second half, with Mbappe in a better position.
Then Messi lit up Parc des Princes with a glimpse of things to come, at the stadium where he scored his last Champions League goal for Barcelona last season.
Guardiola said his team played well but that it was impossible to keep a lid on a players like Mbappe, Messi and Neymar.
"We cannot control them for 90 minutes. The only way I know -- there are two ways actually, is first defend and pray, and the second is to have the ball and create and that's what we did. But we have to create more and be more aggressive," the Spaniard said.
"I wish [Messi] the best, I hope that he's happy and enjoying it here. He made me so happy when we were together."
PSG tops Group A and is level with Club Brugge with four points, while City is third with three points. Club Brugge won 2-1 at last-place RB Leipzig.