Batlles, 34, who spent six seasons at Toulouse from 1993-99, headed in for the visitors in the 34th minute after an Albin Ebondo cross from the right.
"We struggled a bit in the second half and it was not easy to keep Toulouse at bay," St Etienne coach Christophe Galthie told Foot Plus TV after his side produced some impressive attacking football.
"We beat the leaders, we accumulate points, it's a good thing."
Toulouse, who won their opening four games, still top the table on 12 points. Stade Rennes, who beat Sochaux 2-1, are one point adrift while St Etienne lie third on 10 points.
Olympique Lyon, already beaten twice this season, drew 1-1 at home after Gaetan Bong of Valenciennes cancelled out Jeremy Pied's first-half opener.
Paris Saint-Germain rallied from two consecutive defeats by hammering promoted Arles-Avignon 4-0 thanks to a Nene double, Guillaume Hoarau and Mamadou Sakho.
Lille, who had drawn four games, snatched a 4-1 win at neighbours Lens.
The visitors prevailed with doubles by Gervinho and Pierre-Alain Frau after Lens were reduced to nine men following the dismissals of Sebastien Roudet and Issam Jemaa either side of the interval.
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