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."
