The world number eight, who reached the final of the U.S. Open last time out, fought through a tricky tiebreak before sealing a pivotal break to go 4-3 up in the second set.
The break was part of a run of 12 unanswered points for the Japanese, the first man from an Asian country to reach a grand slam singles final, which swung the contest in his favour.
The victory for the 24-year-old, who has also won titles in Barcelona and Memphis this year, boosted his hopes of becoming the first Asian man to compete at the ATP Tour Finals in London in November.
Nishikori is currently sixth in the leaderboard with eight spots available for the prestigious season-ending event.
"It was a tough match," Nishikori said after sealing his victory in one hour and 47 minutes.
"After I won the first set, I relaxed and was able to play attacking tennis.
"I am aiming to win the next tournament in Japan as well," he said, referring to the hardcourt tournament beginning in Tokyo on Monday.
For the 32-year-old Benneteau, it was simply more Malaysian misery.
The loss was his third straight in the final of the Kuala Lumpur event and meant a 10th runners-up prize in his career as the wait goes on for a first ATP Tour title.
"Kei was simply too good in the key moments, especially at the end of the first set," Benneteau said.
"I had some chances, but against these kinds of players, they are small chances and you have to take them. I tried to play my best and I almost did it.
"I'm disappointed with the loss, but very happy with the level of my game. It's hard to keep that level of intensity in every point and every game. I need to improve this to be more consistent," Benneteau added.
(Writing by Patrick Johnston/Amlan Chakraborty; Editing by John O'Brien)
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