The Dane won 4-6, 6-3, 6-1 against Pennetta, and next will face another Italian: French Open winner Francesca Schiavone, who had a 6-4, 6-3 victory over former world's No.1 Dinara Safina.
The major casualty of Thursday's play was fourth-seeded Russian Elena Dementieva, who was beaten 7-6 (3), 6-4 by China's Zheng Jie.
The weather turned cool for the evening session after a brief rain delay, but it didn't stop Wozniacki from notching her fourth win in as many matches against Pennetta.
In the top half of the draw, Kim Clijsters breezed into the quarters with a 6-2, 6-1 win over Kaia Kanepi.
Clijsters, who won the title in Cincinnati last week, was coming off a tougher second-round meeting with American Bethanie Mattek-Sands, which the Belgian won in three sets.
"I was playing an opponent who could not miss a shot, while today Kanepi was missing a lot, especially since her strengths are usually her serve and her backhand," Clijsters said. "I really felt that I had opportunities once I was in a rally with her, and she was either going to make a mistake or I could really try to make her move.
"It's always nice to win a tournament and gradually feel your level improve and also to have a matches like (Mattek-Sands) and in Cincinnati _ to be behind and fight back and win."
Clijsters will face Vera Zvonareva in the last eight, after the eighth seed from Russia downed Agnes Szavay of Hungary 6-3, 6-3.
Svetlana Kuznetsova had a 6-4, 1-6, 6-3 victory over Poland's Agnieszka Radwanska, turning around the match after getting thrashed in the second set.
So what did she do during the break?
"I take a vodka shot, no?" Kuznetsova said with a laugh. "No, nothing like that. ... I just go to the locker-room, change all my clothes, eat a banana and I go back. It's very simple. It was 6-1, but almost every game was deuce, so it was pretty hard. I took a break and it worked."
The win put 11th-seeded Kuznetsova into a quarterfinal Friday against Zheng.
In other matches, 10th-seeded Victoria Azarenka downed ninth-seeded Li Na of China 6-3, 6-3, and 17th-seeded Marion Bartoli of France ousted Czech qualifier Iveta Benesova 6-0, 6-1, who was coming off an upset win over top-seeded Jelena Jankovic.
Azarenka and Bartoli will face off in the quarterfinals.
It has been a difficult year for Kuznetsova, who was the first Russian woman to win the U.S. Open in 2004 and added a French Open title last year.
Back at Roland Garros as defending champion in May, Kuznetsova was beaten in the third round and the massive loss of points dropped her to 19th in the world ranking. Then she went down in the second round at Wimbledon.
When she crossed to North America for the hardcourt season, things seemed to turn around. It was capped by a tournament win in San Diego two weeks ago, when she beat Radwanska in the final.
"I'm not used to having (played) so few matches," Kuznetsova said. "It's hard because the other players had so many matches from the start of the season."
Her promising form may also bode well for the U.S. Open, which begins Aug. 31 in New York. As well as her victory, she also was reached the final in 2007.
Clijsters will start favorite against Zvonareva, although the Russian won their last meeting, in the Wimbledon quarterfinals this year.
"We always had tough matches, a lot of three-setters or very tough ones," Zvonareva said. "I never managed to beat her and finally, at Wimbledon, I was able to play consistently.
"I always believe I could beat anyone on the other side of the net. You have to come out there and not only know the game plan, but be able to execute it. It is very important to play your best to beat someone in the quarter-finals in such a big event."