The 22-year-old was coming off the biggest victory of her career in Berlin on Sunday and would have been the 14th seed in the Italian capital.
She enjoyed a stunning tournament in Germany beating world number one Justine Henin and former number one Serena Williams before also bettering compatriot Elena Dementieva in the final.
Her withdrawal meant that Austrian Sybille Bammer becomes the 19th seed while Russian Ekaterina Makarova comes into the draw as a lucky loser.
Safina was the fourth seed to pull out of the event following the withdrawals of Henin, Amelie Mauresmo and Shahar Peer.
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