Sweden striker Ibrahimovic was shown a straight red card 21 minutes from time after a high kick on keeper Stephane Ruffier's chest as he was chasing the ball.
PSG, who have 22 points from 11 games, were already 1-0 down after Mamadou Sakho had deflected a Pierre-Emerick Aubameyang cross into his own goal 10 minutes into the second half.
Aubameyang put the result beyond doubt in the 73rd, beating Salvatore Sirigu from close range after being set up by Alejandro Alonso.
Striker Guillaume Hoarau pulled one back with two minutes left when he controlled the ball from a Javier Pastore free kick before firing past Ruffier.
"The red card is not deserved because he was not looking at the keeper, but at the ball," coach Carlo Ancelotti said.
"In the dressing room, he did not say anything, he was disappointed. But the problem was before (the red card). We had no pace. St Etienne played better than us and they deserved to win."
PSG suffered a double injury blow in midfield as Blaise Matuidi was replaced by Bodmer shortly before halftime and Clement Chantome suffered a possible ankle injury and was substituted by Mohamed Sissoko after the break.
Asked about Matuidi, Ancelotti said: "It's not serious, he just took a big knock."
PSG will be back at the Parc des Princes on Wednesday to take on Dinamo Zagreb in the Champions League.