As Ligue 1 goes into a three-week break, OM are third with 38 points, behind pacesetters PSG and second-placed Olympique Lyon on goal difference.
Saint-Etienne, who last beat OM at the Velodrome in 1979, are 10th with 27 points from 19 matches.
The game got off to a rather dull start with neither team creating chances and Marseille looking cautious having lost their last two home games.
Marseille, however, went ahead on the stroke of half-time when Ghana striker Ayew, who will play in the Africa Cup of Nations with the Black Stars from January 19 to February 10, headed home from a Rod Fanni cross.
Josuha Guilavogui was set up by Pierre-Emerick Aubameyang but Steve Mandanda dived into the midfielder's feet to deny Saint-Etienne an early opportunity to equalise two minutes into the second half.
Fanni cleared Aubameyang's strike off the goal line 15 minutes from time to keep his team ahead.
Andre Ayew then came close to doubling the tally in the 85th minute after being set up by his younger brother Jordan, only for his low shot to be blocked by Stephane Ruffier.
Earlier, Valenciennes moved up to sixth on 29 points after goals by Gregory Pujol and Jose Saez gave the Northerners a 2-1 win against visiting Evian Thonon Gaillard.
Toulouse, who had bagged only four points from their last eight games, beat Sochaux 2-0 courtesy of goals by Adrien Regattin and Emmanuel Riviere.
On Saturday, PSG claimed a 3-0 win at Stade Brest and Lyon beat Nice 3-0 at home.
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