The biggest upset though was the departure of former world number one Jankovic.
On Thursday though, the Serbian said technical and tactical issues, not physical problems, were behind her loss.
"I'm healthy now. It's just a matter of getting matches and playing, being in this kind of situations, you know, challenging myself," Jankovic told reporters.
"Hopefully I will do better in my next tournament (next week in Montreal). That will be my last preparation tournament before the U.S. Open."
Wozniacki was up 4-3 in the first set but then Bartoli rallied to claim the opening set and dominated the second where she won 14 of 16 first-serve points.
Bartoli will meet Sharapova in the quarter-finals.
Wozniacki flew to Ohio after winning last week's Danish Open and said she may have paid the price for the demanding schedule.
"Definitely it was a factor, there is no doubt about that, getting here late and then getting used to the weather and playing outdoors," she told reporters.
"But it was my choice to play there and then come here."
The only other top 10 seed, apart from Sharapova, to have survived the cull is fourth seeded Belgian Kim Clijsters, who will face Pennetta on Friday having crushed 18-year-old American Christina McHale 6-1 6-1.
(Editing by Frank Pingue/Greg Stutchbury)