The American had been due to play China's Li Na in the first semi-final but said she was pulling out as a precaution.
"On Friday morning I felt a bit of pain in my lower back and if it's not 100 per cent it's better not to play and make it worse," the world number six said.
"But I am in good form, I have a few days to get better and I am confident I will be 100 per cent fit for the French Open."
Williams played only four games in the previous round as Flavia Pennetta of Italy retired with a wrist problem.
"Yesterday I might have had to retire as well," Williams said. "I don't know because we only played a bit and I didn't have time to check my condition."
When she won the title in Madrid last weekend, Williams described her male counterparts as "weenies" for complaining about the slippery nature of the blue clay, saying the women were "way tougher than men".
But on Saturday, the former world number one admitted she might have to eat her words.
"I guess it turns out I was the weenie," she said via Twitter.
Williams, who also won a claycourt titles in Charleston recently, said she needed to be careful not to over-play, having been out of the game for a year in 2010 and 2011 because of a blood clot on one of her lungs.