To the best of my knowledge, the phrase “the ghost in the machine” was first coined by philosopher Gilbert Ryle, as a description of Cartesian dualism, in his 1949 book, The Concept of Mind. Wiki seems to agree. However, for an expression from a relatively recent, academic philosophy book, it has had a remarkable degree of penetration into pop culture. Does anyone here know of any earlier incarnations of the phrase, before Ryle?
I don’t know anything about it, but it sounds like a play on “Deus ex Machina,” which dates back the ancient greeks.
There is a phrase “give up the ghost” with usage going as far back as 1535 (to die) and 1832 (to stop working). source
Its usage of ghost seems similar as in “ghost in the machine,” though I don’t know if there is any relation otherwise.
It’s a great turn of phrase, and if it was Ryle’s first, I’m not surprised to see that it’s resonated widely. Anyway, most of the pop culture references follow after the Police used it for the title of a #2 pop album in 1981.
Maybe, but the meanings are quite different. At least in my definitions 
Deus Ex Machina means, in my mind, “A seemingly unsolvable problem is solved by God (or some other greater force) just jumping in and waving his (or her, or their, or its) hands”
Ghost in the Machine means “The paradox involved in having inanimate matter (organic or mechanical) possessing consciousness or a soul.”
“give up the ghost” reflects the somewhat archaic use of “ghost” in the generic sense of “spirit” as opposed to the modern much more restricted sense of “apparition of presumably dead person”. Hence we have the archaic phrase “ghostly father” that shows up in Romeo and Juliet as well as the not so archaic name “Holy Ghost” for the 3rd member of the Trinity.
Of course, the rationale behind formation of “ghost in the machine” phrase need not have been love for creative anachronisms. Leaving aside facetiousness, you could argue that “ghost” is something much more definite and empirically provable than “spirit”. Kind of like “electricity” is just an abstract notion in the textbook while the “spinning electric motor” or “sudden death through electrocution” have a certain undoubtable reality to them.
Those interested in this stuff should read the related entries Ghost in the Shell and Ship of Theseus.