The 29-year-old Llodra was playing in his eighth final and took his first title since beating Robin Soderling at Rotterdam two years ago.
Llodra was runner-up to Jo-Wilfried Tsonga in last year's Open 13 final and beat Soderling in the quarterfinals this time.
"It's unbelievable to finally win a final in France after losing here and in Lyon last year," Llodra said. "The conditions in Marseille are great for my game. I served very well and was solid throughout the whole match."
Benneteau, playing for his first ATP title, lost in his fourth career final. He also lost at Kitzbuhel and Casablanca on clay and at Lyon's indoor tournament.
"Today, Mike was playing very well. You need to play an exceptional match if you want to beat him," Benneteau said. "He was serving very well, using different angles and different speeds. And even if I returned well, he answered with great volleys."
Benneteau looked tired after his nearly 3-hour marathon semifinal against Tsonga, losing his serve once in each set and failing to create a single break chance against Llodra's serve.
"I was a bit tired mentally," Benneteau said.