Nishikori made a perfect start to the match when he broke Benneteau in the first game to take control of the opening set.
He did not relinquish that control either, losing just one point in each of his next four service games before eventually sealing the opener 6-4 with his fourth set point.
Benneteau had a chance to hit back early in the second set, but he squandered three break points before going on to lose his next service game to hand Nishikori the initiative.
The world number 19 then broke his opponent again to take a commanding lead, before serving out the match and taking the second set 6-2.
Nishikori will face another Frenchman, Jo-Wilfried Tsonga, in the second round.