The 2006 champion lost 6-3, 3-6, 6-4 to the 26th-seeded Italian on Friday. Sharapova had been 12-0 in three-set matches this year, including her first-round win.
Pennetta broke serve to clinch the victory in a match full of breaks, with the third-seeded Russian struggling with her serve.
Sharapova had reached her first Grand Slam final since 2008 shoulder surgery when she was the runner-up at Wimbledon.
Pennetta will next face 13th-seeded Peng Shuai of China, who beat 19th-seeded Julia Goerges 6-4, 7-6 (1).
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