The "flat pack" marble church will go on show as part of the Oxford museum's summer show of more than 200 objects rescued from the bottom of the sea.
Among the other exhibits will be Roman portrait heads and bronze battering rams from the prows of Roman warships.
The Storms, War and Shipwrecks exhibition opens on 21 June 2016.
The treasures on show have been uncovered over the past 60 years since scuba diving made sustained underwater exploration possible.
The exhibition will also explore the work of one of the earliest pioneers of underwater archaeology, Honor Frost (1917-2010).
The reconstruction of the Byzantine church interior will feature marble items raised from a wreck off the southeast coast of Sicily in the 1960s by German archaeologist Gerhard Kapitan.
Among the hundreds of objects recovered were 28 columns with Corinthian capitals and bases, choir-screen slabs and pieces of a pulpit.
Remains of similar churches can be seen today in Ravenna, Italy, in Cyprus and in Libya.
Under the rule of the Emperor Justinian (c.482-565) ships laden with prefabricated marble church interiors were sent out to sites in Italy and north Africa to help spread  Christianity across his empire.  Some became unbalanced and sank during stormy weather.
Dr Paul Roberts, the Ashmolean's head of antiquities, said visitors would be taken on journey "through Sicily's fascinating history".
"Here at the Ashmolean, for the first time, this story will be told exclusively through spectacular finds from the sea, because it is the sea which has always been the lifeblood of the island's unique and diverse culture."
The Ashmolean's 2016 programme also includes an exhibition of some 100 paintings, sculptures and drawings by Andy Warhol - from a private collection in the US - which have never been seen in public.
Curated by Sir Norman Rosenthal, and spanning Warhol's entire output from his 1960s Pop Art to the experimental works of the 1980s, the show will run from 4 February to 15 May 2016.
A Byzantine church raised from a Sicilian shipwreck is to be reconstructed for an exhibition at the Ashmolean museum next year.