The four times champions, who have 44 points from 18 games, remain the only unbeaten side in the major European leagues this season but failed to score for the first time this season.
Les Verts, who have not beaten Lyon since a 3-0 home victory on April 6, 1994, have not won in their last four league outings and stay ninth with 26 points.
In a tense Geoffroy-Guichard stadium, St Etienne fans unveiled a banner summing up the rivalry between the two clubs. It read: "Don't let an agonising Lyon suffer. Shoot them down."
However, after a sluggish start Lyon took control of the midfield marshalled by Juninho and Mali's Mahamadou Diarra.
On 17 minutes, Norway striker John Carew volleyed an Anthony Reveillere cross from near the penalty spot only for his attempt to be parried by St Etienne goalkeeper Jeremie Janot.
The home side's only chance came on the stroke of halftime when midfielder Loic Perrin's 20 metre shot was blocked by Lyon keeper Gregory Coupet.
PERFECT COUPET
Seven minutes into the second half, Janot tipped over a powerful 30-metre Juninho trademark free kick.
The hosts struck back 18
Earlier, Monaco had to settle for a goalless draw at Nantes after their Togo striker Emmanuel Adebayor missed a first-half penalty.
The principality team are now sixth with 28 points just four points behind second-placed AJ Auxerre, who slumped to a 1-0 defeat at Olympique Marseille on Saturday.
The draw allowed Nantes to climb three places to 12th on 22 points, 10 above the relegation zone.
On Saturday, Paris St Germain moved above Monaco and Racing Lens into fourth place as a 2-0 home win over Stade Rennes thanks to Pauleta's double took them onto 30 points.
Girondins Bordeaux stayed third, just a point above PSG, after losing 1-0 at promoted Le Mans.
RC Lens stretched their unbeaten run to 17 games in Ligue 1 when they held fellow northeners Lille to a goalless draw.
Lens, who have not lost a domestic league match since a 2-0 defeat at Nantes in their first game of the season, dropped one place to fifth with 29 points.
Ten-man Racing Strasbourg clinched their first win of the season 2-1 at Nancy to leave Metz, who drew 1-1 at Sochaux, bottom on goal difference with 11 points.
