The world number 31 suffered ankle and wrist injuries during a heavy fall in game 11, and although he tried to continue, Benneteau eventually threw in the towel with the Scot leading 6-5.
It was a sad end to what had been an enthralling match which concluded with third seed Murray through to face either Tomas Berdych or Kei Nishikori in the last eight.
The pair had played each other twice before, with Murray winning both matches.
And the world number four broke in just the second game of the opening set after Benneteau hit a forehand long.
But the Scot found life tough on his next service game and a series of sloppy errors allowed Benneteau five break-point opportunities, with the Frenchman taking advantage on the fifth when Murray put a forehand wide.
The players continued to entertain the crowd with a mixture of tense rallies, wonder shots and wild returns as they battled to gain the upper hand.
Murray, who had beaten Viktor Troicki in just 67 minutes in the previous round, showed signs of improvement when he held serve to love in game seven.
However, drama followed in the 11th game when, with Murray leading 30-0 on serve, Benneteau slipped and landed awkwardly while chasing a wide forehand.
The Frenchman collapsed in agony and a lengthy delay followed as he received treatment and some heavy strapping to his right ankle.
Benneteau decided to continue, although Murray quickly served out the game to take a 6-5 advantage.
The trainer then reappeared to assess Benneteau’s right wrist and forearm, which was also causing the player discomfort.
More strapping was applied, but Benneteau looked in some pain and admitted defeat soon after.