Benneteau's fitness was thrown into doubt when the 30-year-old took a tumble on the clay court, where he appeared to twist his ankle and hurt his wrist in the process.
The Frenchman had both his wrist and ankle strapped up but the pain was too much for the world number 33 and the match was retired on 6-5 in the first set.
The Scotsman got off to a bright start in Monaco, snatching the first break of the contest but his French opponent managed to force a break back instantly.
Murray, who suffered a blister on his finger, relinquished his two-game lead after a number of impressive forehand shots ensured that Benneteau continued to hold his serve.
Despite holding off the British number one, Benneteau suffered the injury blow before either opponent could claim a set lead.