The Dane has been No. 1 in the WTA rankings for almost the entire season but never really challenged her Slovak opponent on Court Suzanne Lenglen, having her serve broken five times.
"She played very, very well today, better than me for sure," said Wozniacki, who had never before lost a set to Hantuchova in three previous matches. "She knew what she was going to go out there and do. She was just too good."
Following No. 2 Kim Clijsters' loss on Thursday, it is the first time in the Open era that the top two seeded women failed to make the round of 16 at a Grand Slam tournament.
Sam Stosur, last year's French Open runner-up, was also eliminated, but 2010 champion Francesca Schiavone advanced to the fourth round. On the men's side, 16-time Grand Slam champion Roger Federer had 10 aces and only 20 unforced errors in a 6-1, 6-4, 6-3 win over No. 29 Janko Tipsarevic.
Wozniacki came into the French Open after winning the clay-court title at the Brussels Open. During the final, she called for a trainer and had her left thigh bandaged.
Although she played the first two rounds at Roland Garros with the same thigh bandaged, she was not wearing any protection on her leg Friday.
But injured or not, the Grand Slam drought remains -- even though Wozniacki said she is not concerned with what others think.
"The only one I feel pressure from is myself to go and give my all for every match and, obviously, I'm a competitor," Wozniacki said. "I love winning. I don't like losing."
Hantuchova beat a current No. 1 player for the first time in her career after six previous losses, including one against Wozniacki this season.
Federer, who won the French Open two years ago to complete a career Grand Slam, again had his serve working, landing 67 percent of his first serves and winning 84 percent of those points.
"So far in this tournament, I've been doing good job, but it's really only at the end of the tournament where I would think it really matters how I did," Federer said. "Right now it's important to keep that up and do that against the best players out there."
Seventh-seeded David Ferrer also won, beating No. 31 Sergiy Stakhovsky of Ukraine 6-1, 6-1, 6-3. No. 9 Gael Monfils of France and No. 13 Richard Gasquet of France also advanced, while Albert Montanes of Spain defeated No. 12 Mikhail Youzhny of Russia 6-1, 7-6 (0), 6-1 and Fabio Fognini of Italy beat No. 30 Guillermo Garcia-Lopez of Spain 4-6, 6-3, 6-3, 6-1.
Stosur was knocked out by Gisela Dulko of Argentina 6-4, 1-6, 6-3. The eighth-seeded Australian struggled early but easily won the second set to take back control. The 51st-ranked Dulko then put herself back in the match by breaking to take a 4-2 lead in the third. She then held twice to advance.
"I was trying to be very aggressive, and I did it very well," Dulko said. "And I think after I have a few ups and downs, and I was lucky to play very good tennis at the end of the match."
Stosur, who also reached the semifinals at Roland Garros in 2009, had 35 unforced errors in the match on Court Philippe Chatrier.
"She seemed to be out ahead a little bit better and really kind of be the one dictating the points, which, for me, I'm usually the one able to do that," Stosur said. "Pretty much right from the first game she kind of set that tone, and it was very difficult for me to turn that around."
Schiavone was broken at the beginning of her match, but then won five straight games to take the first set and eventually the match when opponent Peng Shuai of China retired while trailing 6-3, 1-2.
Peng called for a doctor after the first game of the second set and had her blood pressure checked. She looked exhausted in her chair and then started to cry but broke for a 2-0 lead.
Schiavone won the next game before her opponent quit.
"I've been just sick for three or four days," Peng said, adding that she has had a fever. "So it's tough for me to play. I was really tired. I was really sick so my body could not really handle that."
"Now it's starting to be more complicated matches," the 13th-seeded Russian said. "I pass three rounds, so next round going to be hard. Just have to focus and start to play better."
No. 10 Jelena Jankovic reached the fourth round with a 6-2, 6-2 win over Bethanie Mattek-Sands of the United States, while No. 11 Marion Bartoli of France, a former Wimbledon finalist, defeated No. 17 Julia Goerges of Germany 3-6, 6-2, 6-4.
Two other Russians also advanced, No. 3 Vera Zvonareva and No. 14 Anastasia Pavlyuchenkova.