The 11th-ranked Italian, who had lost both previous matches against Shaughnessy, broke the American's serve five times.
Pennetta holds eight WTA Tour titles but is yet to win an indoor event.
She next plays Anna-Lena Groenefeld of Germany, who defeated Roberta Vinci of Italy 7-5, 6-1.
Julia Goerges of Germany beat sixth-seeded Sorana Cirstea of Romania 6-3, 6-3. The 79th-ranked Goerges converted six of 13 break points against Cirstea, who struggled with her serve throughout the match.
Eighth-seeded Sara Errani of Italy advanced by beating Arantxa Parra Santonja of Spain, 6-2, 6-3.
Also, Olga Govortsova of Belarus beat Petra Martic of Croatia 6-2, 6-7 (7), 6-2, and Tatjana Malek of Germany defeated Aravane Rezai of France 7-5, 7-5.
Errani, Pennetta set up all-Italian Palermo finalVan der Vaart admits Ajax snub
