The "debilitating" sting forced her to abandon the 166km (103-mile) swim after 11 hours, her support team said.
It added that the athlete would need 24 hours to recuperate from the severe injury.
Ms McCardel earlier described the swim as "the hardest in the world today".
She had hoped to complete the distance in about 60 hours.
Ms McCardel's team said on Wednesday evening that she had been taken to one of her support vessels and was sailing toward Key West.
Her failed try comes almost a year after American swimmer Diana Nyad abandoned her fourth attempt at the same feat.
Ms Nyad, 62, was pulled from the water after she had been stung repeatedly in the face by jellyfish and was buffeted by strong waves and currents.
"It's a tough night for Chloe McCardel, a superior swimmer and an exemplary spirit," Ms Nyad wrote in a post on her Facebook page.
"I send Chloe congratulations for her many months of training and her courageous foray into those dangerous waters."
Ms McCardel jumped into the water from Havana's Marina Hemingway at 10:00 local time (14:00 GMT).
The athlete from Melbourne had covered about 19km by late afternoon, being monitored by coaches and doctors from onboard boats.
Speaking at a news conference on Tuesday, Ms McCardel said she had been training for this particular swim for six months, and had spent a lot of time "analysing the reasons and mistakes" which had prevented other swimmers from completing it.