The Argentine played a lovely one-two with Kylian Mbappe before a trademark finish in the second half after Idrissa Gueye had netted in the first for the hosts.
Bernardo Silva missed a sitter for the visitors, and here Sportsmail assesses the performances of the players in the French capital.
Lionel Messi scored his first goal for Paris Saint-Germain as they beat Manchester City
Gianluigi Donnarumma – 6.5
Made a number of decent stops. Did seem strangely uneasy with some second-half crosses for a man of his stature.
Achraf Hakimi – 7.5
Some courageous covering from right back, a bundle of energy and strong in the challenge.
Marquinhos – 7
The PSG captain was strong in the air when he needed to be. Made sure his back four stayed narrow.
PSG captain Marquinhos was strong in the air when he needed to be at the Parc des Princes
Presnel Kimpembe – 6.5
Nobody completed more clearances than Kimpembe’s five in the first half as City controlled the game.
Nuno Mendes – 6
Looks more comfortable going forward and allowed Riyad Mahrez to sneak in behind too often.
Ander Herrera – 6
Unusually prolific so far this season and is given far more licence to roam forward to join in.
Idrissa Gueye – 8
His night was so much more than merely scorching home the opener. Such a clever midfielder.
Idrissa Gueye’s night was so much more than merely scorching home the opening goal
Marco Verratti – 7.5
Again displayed why he is one of the finest around. Screens intelligently and carried possession well.
Lionel Messi – 7.5
Exceptionally quiet, just could not get into the game – and then he sealed it with a stunner.
Kylian Mbappe – 7
Strong link up play and that was evident for the first goal as he dropped off the front to good effect.
Neymar – 6.5
More disciplined than you might imagine and then takes at least two men with him when roaming.
Kylian Mbappe had strong link up play and that was evident for the first goal from the hosts
Gini Wijnaldum (for Verratti, 78)
Danilo (for Gueye, 90)
Subs not used: Navas, Letellier, Paredes, Icardi, Dagba, Wijnaldum, Kurzawa, Diallo, Draxler, Kehrer, Ebimbe
Manager: Mauricio Pochettino – 7
Made sure that his midfield put in the work to counter City. Even the two superstar wide men tracked back on occasion.
MANCHESTER CITY (4-2-3-1)
Ederson – 6
Not a lot he could do about Gueye’s strike. Rarely called upon but ended up conceding twice.
Kyle Walker – 6
Could have been utilised on the overlap more often. Completed his defensive tasks well against Neymar.
Ruben Dias – 6
Strangely silent and lacking communication when PSG opened City up in the eighth minute to take the lead.
Ruben Dias was strangely silent and lacking communication when PSG opened City up
Aymeric Laporte – 7
Passing out from the back was exemplary. Has started this season as if he really means business.
Joao Cancelo – 6.5
Did a decent job on Messi to begin with. Did threaten going forward without much end product.
Bernardo Silva – 6
Another all-action display but will not believe he managed to hit the bar from two yards out.
Rodri – 7.5
The Spaniard continues to improve at the base of midfield. Dominant in his duels once again.
Bernardo Silva will not believe he managed to hit the bar from two yards out in his display
Riyad Mahrez – 6.5
Wrongfooted for Gueye’s goal, although looked dangerous from the right in an attacking sense.
Kevin De Bruyne – 6.5
Might consider himself fortunate not to see red. Some moments of audacious quality in the final third.
Jack Grealish – 6
Often stopped in his tracks as PSG doubled up on the winger. Cut a frustrated figure as decisions when against him.
Raheem Sterling – 6.5
An encouraging performance as a central striker. Trying to recapture his form, Sterling was a nuisance.
Jack Grealish was often stopped in his tracks as PSG doubled up on the £100m winger
Phil Foden (for Grealish, 68) – 6.5
Gabriel Jesus (for Sterling, 78)
Subs not used: Steffen, Carson, Stones, Ake, Torres, Fernandinho, McAtee, Wilson-Esbrand
Manager: Pep Guardiola – 6.5
A defeat did not do his team justice in truth. City were in control for large spells and will go back to Manchester happy with the performance.
Referee: Carlos del Cerro Grande (ESP) – 5
Allowed a lot go. Guardiola may feel aggrieved at the balance of decisions on the night – even though De Bruyne could have been off.