From the Latin "Hoc est Corpus" - The medieval priest holding up the bread and water and turning it into the body and blood of Christ. Hence the ignorant or superstitious peasant adapted "Hocus Pocus" to apply to any magical act of transmutation or change, the classic mockery of power and authority.
There are alternate theories of the etymology, according to Sharon Turner in The History of the Anglo-Saxons, they were believed to be derived from Ochus Bochus, a magician and demon of the north, and the old Oxford English Dictionary attributes the term term to an abbreviated "hax pax max Deus adimax", a pseudo-Latin phrase used as a magical formula by conjurers.