The Purple Rain icon performed in Atlanta, Georgia on Thursday night as part of his stripped-back Piano and a Microphone tour.
But the plane made an unscheduled landing at Quad City International Airport in Moline, Illinois just hours later after he fell ill.
The 57-year-old is believed to have had been fighting flu for several weeks but sources claim he "felt considerably worse" on the flight.
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He was taken to a nearby hospital for treatment but released three hours later, according to a spokesman for Prince.
The hitmaker, who released his most recent album Hit n Run Phase One in September, is now recovering at home.
Several messages were posted from his Twitter account yesterday but they have all been deleted, according to reports.
Last month Prince revealed to an audience at a show in New York he is writing a memoir called The Beautiful Ones.
He said: "This is my first [book]. My brother Dan is helping me with it. He's a good critic and that’s what I need. He's really helping me get through this."
The book, described as an "unconventional and poetic journey through his life", will be released next year, according to publishing house Spiegel & Grau.