Cedric Faure stunned the home side with an eighth minute opener, however Kanga Akale levelled matter just six minutes later.
French international striker Cisse scored his first just before the break and then doubled his tally on 66 minutes with what proved the winning goal.
Eduardo Da Silva did pull one back late on, however Toulouse failed to find that all-important equaliser.
Paris Saint Germain's title chase took a turn for the worse following a 1-0 defeat at the hands of Lens.
Charles-Edouard Coridon was the hero netting the only goal after 32 minutes at Lens' Stade Felix-Bollaert.
Elsewhere, the points were shared at Marseille after Camel Meriem cancelled Juan Pablo Francia's early opener, to earn a 1-1 draw at Stade Velodrome.
Click below for match summaries:
Auxerre 3-2 Toulouse
Lens 1-0 PSG
Marseille 1-1 Bordeaux
Click here for the latest Championnat table.
