The victory, coming after a run of four games without a win, puts L’OM second in the Ligue 1 table, but only behind leaders Monaco on goal difference.
Elie Baup’s side took the lead after 22 minutes when Benjamin Mendy got on the end of a cross from Mathieu Valbuena to send the ball looping over the head of keeper Stephane Ruffier.
Four minutes later, Giannelli Imbula doubled their lead when he converted from a Rod Fanni cross to finish off a flowing team move.
Faouzi Ghoulam pulled one back from the penalty spot after Alaixys Romao handballed from a Yohan Mollo cross but St Etienne could not complete the comeback to pick up a first win in Marseille since 1979.
In Tuesday night’s other match, Lille defeated Evian 3-0 at home to go third, one point behind Marseille.
Goals from Salomon Kalou (12) and Ronny Rodelin (72), plus an own goal from Jesper Hansen (32), saw Lille safely home.