Les Verts climbed from fourth place to second on 26 points and trail leaders Olympique Lyon, who host champions Montpellier on Saturday, by two points.
Ajaccio are 16th on 16 points, two points above the relegation zone.
St Etienne enjoyed most of the possession in a game hampered by rain and gusty winds but they were toothless up front.
Adrian Mutu had a good chance for Ajaccio in the first half when his header shaved Stephane Ruffier's post. The Romanian was then replaced on the hour mark.
St Etienne's Brazilian striker Brandao went off 15 minutes from time because of a strained leg muscle.
Next week Christophe Galtier's side host arch-rivals Lyon at the Stade Geoffroy Guichard.