Laurent Blanc's side now have 51 points from 24 games, three more than second-placed Montpellier who beat Grenoble 1-0 on Saturday.
Lille, 3-1 winners over Boulogne-sur-Mer on Saturday, are third on 44 points, one ahead of Olympique Lyon who overcame Racing Lens 1-0.
Wendel created the first goal for Bordeaux in the 13th minute, a header from striker Marouane Chamakh.
The Brazilian then shot powerfully home 17 minutes later before Bakary Sako pulled one back for fifth-bottom St Etienne with a free kick from 25 metres on the stroke of half-time.
St Etienne dominated possession in the second half and wasted a host of chances, including a penalty miss by Gonzalo Bergessio in the 71st minute after Chamakh handled.
Wendel made them pay when he converted a cross by substitute Yoan Gouffran with 11 minutes left.
Champions Bordeaux have seen their nine-point lead cut to three since play resumed last month after the winter break and went into Sunday's match looking to repair a sequence of one win in four league outings.
"We struggled (tonight) even when we were ahead," Blanc told Canal Plus television. "We seemed to have a problem of confidence.
"We have to defend better than this (but) the victory will be good for the team because we really needed it."
