Yaroslava Shvedova made the most of blustery conditions and a spectacular loss of form on the part of her opponent to win their fourth round encounter 3-6 6-2 6-0.
After taking the first set, the Chinese seventh seed, seemingly shorn of confidence, collapsed, taking only two games out of the next 14.
Last year's champion made 41 unforced errors as she spectacularly lost control of a match in which she had looked to be cruising towards victory.
The conditions on Court Suzanne Lenglen made serving difficult, but the Kazakh's aggressive approach left Li flat-footed.
Her rhythm went to pieces in the face of an all-out assault from the doubles specialist who was not expected to be a realistic challenger in the singles draw, even in a tournament jam-packed full of shock results.
A clearly disappointed Li had an intriguingly simplistic explanation for why her game went to pieces.
"Nothing happened," she told reporters. "I just tried to play ball back into the court, but I couldn't."
"Right now, I want totally relax the mind and body," she added. "I think I didn't play bad in the claycourt season.
"I need some time to recover. I'm not machine."
Shvedova, who won grand slam doubles titles at both Wimbledon and the U.S. Open in 2010, had signalled her intent coming into the match having not dropped a set in her opening three matches.
Her victory today, however, is a remarkable reversal in fortunes after she spent much of last year recovering from knee surgery that forced her to compete in futures tournaments to regain fitness and confidence.
"I think it's the most incredible win for me," she said.
"I always have nice matches against top players because it's easier, because I have no pressure, and I always come to beat them.
Li has endured a difficult 12 months since beating Francesca Schiavone to lift the Suzanne Lenglen Cup and has now failed to get past the fourth round in all four slams.
"I felt she was a little bit nervous, added Shvedova. "She didn't play like she was playing last year and she was making mistakes.
"Maybe she was thinking a lot or maybe she's not in the best shape."
Having stormed through the second set, the Kazakh broke her opponent's serve three times in the decider, and while she wasted two match points in the final game, she eventually closed it out when Li netted a tame backhand.
She will now play Petra Kvitova after the Czech fourth seed Kvitova continued her quest for a second Grand Slam title by cruising into the quarter-finals with a 6-2 6-1 win over American Varvara Lepchenko.
The Wimbledon champion, whose match was moved from Court Philippe Chatrier to the less fancy Court One as organisers tried to beat dusk on a gloomy day, was never threatened as she saw off the world number 63 in just an hour.
Kvitova, who could meet Russian second seed Maria Sharapova in a potential semi-final clash, ended the contest on her second match point with a forehand winner.
Even for someone who struggles with a game plan, Maria Sharapova was probably surprised that she dropped serve nine times in a topsy-turvy 6-4 6-7 6-2 win over Czech Klara Zakopalova that sent her to the French Open quarter-finals.
Russian second seed Sharapova faced windy conditions and a fired-up opponent to advance, needing more than three hours to subdue the world number 44 and set up a last-eight meeting with either Estonian 23rd seed Kaia Kanepi or Dutchwoman Arantxa Rus.
Sharapova, who hired Thomas Hogstedt in December 2010 to coach her, was full of praise for the Swede, even if she is not the perfect student.
"I'm useless with game plans. That's probably the one thing he just gets so frustrated with me about," Sharapova, who will take over from Victoria Azarenka as world number one if she reaches the final in Paris, told a news conference.
"I go out there and I do my own thing, and then he's like, after the match, 'Really? What's the point of having me?'
"But I apologised when I hired him in advance, so he's okay."
There was nothing Hogstedt could do, however, about the swirling winds that disrupted play on Court Philippe Chatrier.
Twenty-one of the 30 games went against serve as the players sometimes struggled to throw the ball properly and the geranium displays took a beating from gusts of wind.
"The conditions were difficult, so it was a good test for me. I had chances to finish it in two sets, and I didn't," said Sharapova, who is looking to complete her collection of grand slam titles.
However, the Russian acknowledged the conditions were not the only reasons why she struggled.
"She is dangerous. She can play well. When she hits the ball, I think some days she goes out there and goes for it, and it seems like everything just goes in and stays so low over the net," Sharapova said.
"A great example is when I was up in that first match point, she was just drilling the ball. I'm sure some other days she goes out and makes mistakes.
"And that's probably why she came to this tournament not seeded. But she is certainly dangerous."
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