The Swiss star has dropped just one set en route to the last eight where he will play Fernando Gonzalez of Chile for a place in the semi-finals, but he will have cause for concern over how he struggled to kill off his lowly-ranked opponent.
"He played a great match today but it was tough for both us with the conditions," said the top seed.
The unseeded Benneteau had played more sets than any other player to get the last 16 (14) and he was not expected to pose any problems for the world No. 1 who won their only previous meeting in straight sets in Cincinnati last year.
But he did give the home fans, in a damp and overcast Philippe Chatrier Centre Court, something to cheer about when he broke the Federer serve at 3-5 down in the first set.
He failed though to hold on to his own serve in the following game sending a looping forehand wide under pressure from a cracking Federer backhand down the line.
Benneteau gifted Federer the first break of the second set by netting an easy volley at the net and then playing an abysmal drop shot.
But once again the world No.1 failed to put the set away when serving at 5-3 and this time the Frenchman had a point to force a tie-break before Federer struck again moving two sets up as the rain started to fall.
Play resumed ninety minutes later and Federer promptly bagged a break of serve in the third game only for Benneteau to do likewise in the next game.
The Swiss maestro was finding it hard to put away his 55th world-ranked opponent, letting slip a match point at 5-4 up but two games later he finished it off with a smash at the net.
Benneteau said it had been an "exceptional experience playing against Federer on the centre court.
"But I was always behind, that was the problem today and I had few opportunities."
The 26-year-old Federer is bent on winning the only Grand Slam title that has eluded him having lost to Rafael Nadal here in the last three years, including the last two finals.
He came into Paris after a poor season by his own high standards having lifted just one title at Estoril and losing seven times, twice to Nadal on clay.
But he says he is happy with his form and ready to challenge Nadal for the title. Nadal though has so far looked formidable and has yet to lose a set in four matches.
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