The hooded figure was placed inside the Big Thunder Mountain Railroad ride at the California theme park last weekend.
It is understood to have remained in place for 90 minutes before the ride was closed down and the figure removed.
A spokeswoman for Banksy said the stunt was intended to highlight the plight of terror suspects at the controversial detention centre in Cuba.
Banksy is notorious for his secretive and subversive stunts - such as sneaking doctored versions of classic paintings into major art galleries.
In 2005, he embarrassed the British Museum by planting a hoax cave painting of a man pushing a supermarket trolley, which he said went unnoticed for three days.
Last week, he smuggled 500 "alternative" versions of Paris Hilton's album into record shops around the UK.
Topless fake cover
The artist replaced Hilton's songs with his own remixes, which were given titles such as Why am I Famous?, What Have I Done? and What Am I For?
He also changed the artwork to show the US socialite topless and with a dog's head.
The Bristolian is most famous for his graffiti artworks, which are often created in prominent public places.
Last year, he produced nine stencil sprays on the Palestinian side of the West Bank barrier.
The satirical images showed images of life on the other side of the barrier.
One depicted a hole in the wall with an idyllic beach, while another showed a mountain landscape.
Earlier this summer, a piece of Banksy's graffiti art on a Bristol building was allowed to remain in place by the city council after the public voiced overwhelming support.
The stencilled image, which showed a naked man hanging onto a window ledge, won a 97% approval rating from residents on an internet discussion forum.
Banksy is due to hold what is billed as a "three day vandalised warehouse extravaganza" in Los Angeles this weekend.
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