The 31-year-old British number one was not aware he had a problem while suffering a first-round exit at the hands of 18-year-old Murray in Basel last week.
But a subsequent scan revealed he had a rib cartilage problem which could sideline him for up to three weeks.
"Unfortunately, my season has come to a disappointing end as I've been forced to withdraw from the BNP Paribas Masters after picking up another injury," Henman told his official website www.timhenman.org.
"Doctors have confirmed that I've fractured the cartilage of my first rib, which happened during my first round loss to Andy Murray in Basel.
"I didn't feel anything during my match with Andy but the next morning I woke up and knew I was in trouble.
"I went for a couple of scans here in Paris that eventually revealed the problem, and I've been told that it will probably take between two to three weeks for me to recover."
Henman, who suffered a second-round exit against Dmitry Tursunov at Wimbledon, has endured a disappointing year with back trouble and other injuries hampering his form but remains hopeful that he can bounce back next year.
"This year has been really difficult at times as I've had to contend with so many injuries, and at this level if you're trying to compete when not fully fit then it's going to be a real struggle," he said.
"I haven't been able to build up any kind of momentum, although in terms of my back problem, the last few events have been better, which is why it's so frustrating to have suffered another setback.
"The one positive thing is that the season is now over for me, and mentally I can move on and look forward to next year.
"First, I have to recover from this, but once I do that my goal is to work as hard as possible in the off-season so that I can start next year in the best possible shape.
"I'm very motivated and ready to start working hard to get off to the best possible start next year, when I plan to play a full schedule."
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