Halep sustained the injury last month while training for the Wuhan Open, where she lost in the second round. She then retired midway through her opener in Shanghai.
"I really wanted to play here in Moscow, but unfortunately my back is still causing me pain and I don't want to take any unnecessary risks," Halep, who will still end the year as women's world number one, tweeted on Tuesday.
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"While it's disappointing to withdraw, I know it's important to put my health first," the 27-year-old added.
Halep had said on Monday that she would be "very doubtful" for this month's season-ending WTA Finals if her injury prevents her from playing in Moscow.
The French Open champion, who claimed her maiden Grand Slam title this year, was the first player to qualify for the Oct. 21-28 event in Singapore.
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