Lyon, replaced as leaders by Montpellier after their 3-1 victory at Ajaccio, had France goalkeeper Hugo Lloris sent off for bringing down Romain Hamouma on half-time and Benjamin Nivet converted the penalty.
Nivet was dismissed midway through the second half for a second booking but Remi Garde's injury-hit side still suffered their first defeat of the campaign after seven games.
"I'm disappointed, frustrated," coach Garde told reporters.
"I think we didn't start playing until the 43rd minute when we were woken up by a passage of play [Lloris's dismissal]."
Marseille had Loic Remy's headers either side of the break and Guillaume Rippert's second yellow card to thank for a 2-0 win over Evian at the Stade Velodrome to lift them up to 15th from bottom and ease the pressure on coach Didier Deschamps.
Winger Mathieu Valbuena, who set up both goals, is now looking forward to Saturday's trip to Valenciennes.
"There were encouraging signs, I hope this win leads immediately to others," he said. "The fans were exemplary."
Big-spending Paris Saint-Germain are fourth after Nene and Kevin Gameiro netted a penalty each in a 2-1 home win over Nice, who also scored from the spot.
There were goals galore as second-placed Stade Rennes enjoyed a 6-2 triumph at Sochaux, who included scorer Modibo Maiga for the first time since he refused to play after demanding a move.
Toulouse, level on points with Rennes, Lyon and PSG but two behind Montpellier, missed the chance to go joint-top after Paulao headed in a corner a minute from time to give Saint-Etienne a 1-1 home draw.
Champions Lille, four points off the leaders, drew 1-1 at Girondins Bordeaux on Tuesday.
