Messi found the back of the net with his fourth league goal of the season in the fifth minute to put Christophe Galtier's side on 22 points from eight games.
Lyon, who have now lost their last three matches, are sixth on 13 points.
PSG have won nine and drawn one of their 10 games in all competitions and while they have shown less brilliance lately, they were still a cut above at the Groupama Stadium.
The performance, however, was not enough for PSG midfielder Vitinha, who believed they should have put the match to bed.
"I'm satisfied with the result but not with the performance. We could have played better. There's a lot of room for improvement," the Portuguese said. "We should have controlled the match better in the second half and we should have had more chances with the possession we had."
It was a dream start for PSG, who went ahead from their first opportunity with Messi beating Anthony Lopes from just inside the area after collecting Neymar's pass.
The Argentina international had another chance early in the second half, but Lopes this time pulled off a superb save to keep his team in contention.
Neymar and Messi had two more opportunities for PSG, only for Lopes to deny them, but the hosts were never able to threaten again.