The 1-0 home victory moves St Etienne into second in the table with 10 points from five games.
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The hosts came closest in the opening 10 minutes as Kevin Monnet-Paquet looked to provide for strike partner Mevlut Erding, who wasted his chance by lashing straight at the keeper from the centre of the box.
Erding was on hand to threaten again later in the half, but he turned his effort wide of the left post from close range, before Moustapha Bayal Sall somehow flicked his header wide following a cross from Romain Hamouma.
Midfielder Hamouma continued to carve out crosses for his teammates as both Benjamin Corgnet and Monnet-Paquet were guilty of being wasteful with their heads, leaving the teams level going into the break.
St Etienne grabbed their winning goal in the 74th minute, but it was not through great play of their own, as Caen defender Da Silva put into his own net to break the deadlock and condemn his side to defeat.