Saint-Etienne, who are currently bottom of the French top flight, took a shock lead on Sunday with Denis Bouanga scoring the opener.
Lionel Messi, Kylian Mbappe and Neymar all started the match but PSG's equaliser came courtesy of centre-back Marquinhos' header on the stroke of half time after Timothee Kolodziejczak was sent-off for a foul on Mbappe.
But it looked like the ten men were going to hold on for a point until the 78th minute when Angel Di Maria curled the ball in. Marquinhos sealed the three points with a goal in stoppage-time.
Marquinhos was the unlikely hero in front of goal, however, it should be noted that Messi assisted all of PSG's goals.
The win sees Mauricio Pochettino's men go 12 points clear at the top of the table but it may have come at some cost with Neymar going off on a stretcher late on.
Neymar was writhing in pain as he turned his ankle at a sickening angle following a challenge with Saint-Etienne's Yvann Macon.
On the Brazilian's injury, Pochettino said: "Of course, we are worried.
"But we hope that it is nothing too serious and that he can come back to help the team as soon as possible."
The match also saw Pochettino hand Sergio Ramos his first appearance for PSG since joining on a free transfer in the summer.