The couple was set to host and DJ an event on Saturday night.
"We really feel bad, and I work sick when I can, but unfortunately I couldn't drive to Miami, so I'm stuck in New York City with doctor's orders not to fly," Samantha told the mag. "Any reports otherwise are false and unfair."
The gig has reportedly been rescheduled for March 7.
According to a People source, the two are under the weather with ear infections.
"Sam needs her ears, and flying with an ear infection is a risk that she can't really afford to take," the source said.
Lindsay and Samantha were recently spotted in New York for Fashion Week, supporting Samantha's designer sister, Charlotte, at her Bryant Park show.
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