Kakuta converted the spot kick early on at Stade Bollert-Delelis after Timothee Kolodziejczak's trip on forward Ignatius Ganago inside the box.
Florian Sotoca made sure of all three points which send the northern outfit a place off top spot on goal difference in the final 10 minutes after Wahbi Khazri's red card just after the hour mark.
Later on Saturday, Patrick Vieira's Nice, the only side to beat Lens this term, on the opening day of the season, host Nantes looking for their first league win since late-August.
On Sunday, league leaders Rennes welcome Reims and Champions League semi-finalists Lyon face Andre Villas-Boas' Marseille.
On Friday, Neymar scored twice for Paris Saint-Germain in a crushing 6-1 win over Angers.
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